A Tier-1 Indian pharma formulator with plant sites in Baddi, Ahmedabad-Vadodara, Halol and Bachupally must read the 56th GST Council FAQ published alongside the 3 September 2025 Council press release not as reference commentary but as three compliance instructions — Q10 on the deepened inversion for formulators, Q25 on the medical-device HSN 9018-9022 rate transition, and Q51 on the life-saving drugs nil-rate schedule and Rule 42/43 common-credit reversal exposure. Reading Q10 as a compliance instruction drives an immediate switch from a rolling-quarterly RFD-01 cycle to a strict monthly cycle. Reading Q25 mandates per-SKU MRP recalculation and physical re-labelling before the next taxable invoice under DPCO 2013 Para 20 exposure. Reading Q51 flags the nil-rate Rule 42/43 apportionment obligation on shared inputs — a taxable-versus-nil batch attribution flag on the manufacturing register that must be live before the first nil-rate invoice.
For each of Q10, Q25 and Q51, prepare a Council FAQ-anchored one-pager for the board and audit committee that captures four fields — FAQ text verbatim, ERP-field change (which master, which flag, which effective date 22 September 2025), reconciliation cadence (weekly for the medical-device MRP recalculation until complete, monthly for the RFD-01 refund cycle and the Rule 42 apportionment, quarterly for the Rule 43 capital-goods amortisation), and exception-escalation path when the reconciliation breaks. Route each one-pager through the tax head, the plant tax coordinators, and the statutory auditor's engagement lead as observer for the first two cycles. Anchor Q10 to the RFD-01 monthly filing discipline under the amended Rule 89(5) formula. Anchor Q25 to the per-SKU MRP recalculation workflow driven by the price-master file with an inventory-on-hand pause during re-labelling. Anchor Q51 to a batch-level taxable-versus-nil attribution flag on the manufacturing register plus a common-input register that separates fully-attributed inputs from shared inputs plus a monthly Rule 42 apportionment run and a Rule 43 amortisation register for capital goods deployed on nil-rate lines.
SKU master with per-SKU HSN code, output GST rate versioned by effective date (pre-cutover rate valid to 21 September 2025 midnight, post-cutover rate from 22 September 2025 zero hour), pre-recalculated MRP and post-recalculated MRP with re-labelling status flag; input master with input HSN, input GST rate, common-versus-attributed flag, and eligible-versus-blocked ITC treatment; manufacturing register with batch number, formulation identity, taxable-versus-nil attribution flag, and shared-input consumption per batch; common-input register with month-of-consumption timestamp for the Rule 42 apportionment; capital-goods register with date of capitalisation, deployment plant, taxable-nil-common flag, and 60-month Rule 43 amortisation schedule; RFD-01 workbook keyed to a monthly filing cadence with input services and capital goods excluded from the Net ITC numerator; NPPA DPCO 2013 register linking each scheduled formulation to the ceiling price and the MRP recalculated for the post-cutover rate; Council FAQ one-pager register with Q10, Q25, Q51 text, ERP-field change, cadence and exception path.
A month-end pharma Council FAQ compliance pack: Q10 one-pager with the RFD-01 filing draft under the amended Rule 89(5) formula and the input-services plus capital-goods exclusion audit trail; Q25 one-pager with the per-SKU MRP recalculation completion status, the re-labelling inventory pause register, and the DPCO 2013 Para 20 exception log where any SKU invoiced at the new rate before re-labelling completed; Q51 one-pager with the Rule 42 monthly apportionment for shared inputs consumed on taxable versus nil-rate batches and the Rule 43 quarterly amortisation for capital goods deployed on nil-rate lines; a scheduled monthly review meeting minute for the first two cycles with the tax head, the plant tax coordinators, and the statutory auditor as observer, downstepped to quarterly cadence from the third cycle. The pack is the single document the board audit committee signs off against at the quarterly meeting and the single document the statutory auditor tests against at year-end.
A Tier-1 Indian pharma formulator closes its books for the September-October 2025 straddle period with three CBIC FAQ questions open on the tax-head’s desk. Q10 of the 56th GST Council FAQ, published alongside the 3 September 2025 Council press release, tells the controller that the inversion for formulators deepens post-22 September 2025 rather than narrowing, and pairs the acknowledgement with an expedited Section 54(3) refund pledge. Q25 tells the same controller that Maximum Retail Price on every SKU under HSN 9018-9022 must be recalculated and the physical inventory re-labelled before the next taxable invoice under the reduced 5 percent rate. Q51 flags that the specified schedule of life-saving drugs for cancer, HIV, tuberculosis and rare diseases is nil-rated, and that Rule 42 (in-period common-credit reversal) and Rule 43 (capital-goods amortised reversal) apply because a nil-rated supply is treated as exempt supply for the purpose of common-credit apportionment. This is GST Council 56 FAQ Q10 Q25 Q51 pharma clarifications as an operating discipline — the reading pattern that turns a Council FAQ from reference commentary into three concrete ERP-field changes and a two-cycle monthly review cadence with the statutory auditor as first-two-cycle observer.
Quick reference
| Aspect | Detail |
|---|---|
| Council decision date | 3 September 2025 (56th GST Council meeting) |
| Effective rate date | 22 September 2025 (zero hour) |
| FAQ source | CBIC FAQ published alongside the Council press release |
| Q10 subject | Deepened inversion for pharma formulators plus expedited Section 54(3) refund pledge |
| Q25 subject | Medical devices HSN 9018-9022 rate transition (18 percent to 5 percent) plus per-SKU MRP recalculation and re-labelling |
| Q51 subject | Life-saving drugs nil-rate schedule (cancer, HIV, TB, rare disease) plus Rule 42/43 common-credit reversal obligation |
| Post-cutover formulation output rate | 5 percent (HSN Chapter 30 across 3003, 3004, 3005, 3006) |
| Post-cutover medical device rate | 5 percent (HSN 9018, 9019, 9020, 9021, 9022) |
| Life-saving drugs rate | Nil (per specified schedule notified alongside Council) |
| Inversion refund provision | Section 54(3) CGST Act 2017 |
| Refund formula | Rule 89(5), amended by Notification 14/2022-Central Tax dated 5 July 2022 |
| Common-credit reversal rules | Rule 42 (in-period, inputs and input services) and Rule 43 (capital goods, 60-month) |
| MRP recalculation obligation | Per DPCO 2013 Para 20 exposure for scheduled formulations |
| Recommended RFD-01 cadence post-cutover | Strictly monthly for first two cycles, quarterly review sign-off |
The reconciliation in one paragraph
The 56th GST Council decision of 3 September 2025 rationalised the pharma-sector rate structure with three headline moves that took effect from 22 September 2025 — all drugs and medicaments under HSN Chapter 30 moved to a flat 5 percent output rate, medical instruments and apparatus under HSN 9018-9022 moved from 18 percent to 5 percent, and a specified schedule of life-saving drugs for cancer, HIV, tuberculosis and rare diseases moved to a nil rate. The CBIC FAQ published alongside the Council press release addresses each move — Q10 the deepened inversion for formulators and the expedited Section 54(3) refund pledge, Q25 the medical-device rate transition and the per-SKU MRP recalculation obligation, and Q51 the life-saving drugs nil-rate schedule and the Rule 42/43 common-credit reversal obligation. A pharma finance controller reads each Q as a compliance instruction rather than as reference commentary. Q10 drives an immediate switch from a rolling-quarterly RFD-01 filing cycle to a strict monthly cycle with input services and capital goods excluded from the Net ITC numerator per the Notification 14/2022 amended formula. Q25 drives a per-SKU MRP recalculation workflow, an inventory-on-hand pause during physical re-labelling, and an audit-trail entry linking the recalculated MRP to the invoice line that first carries the new 5 percent rate. Q51 drives a per-batch taxable-versus-nil attribution flag on the manufacturing register, a common-input register that separates fully-attributed inputs from shared inputs, a monthly Rule 42 apportionment run keyed to the nil-rate turnover ratio, and a Rule 43 60-month amortisation register for capital goods deployed on nil-rate lines. The three ERP-field changes are captured in three Council FAQ-anchored one-pagers for the board and audit committee, and a scheduled monthly review meeting for the first two cycles includes the statutory auditor as observer to convert management review into contemporaneous audit evidence.
What the scenario looks like in India
The persona for this reading discipline is a finance controller at a Tier-1 integrated Indian pharma formulator with plant sites distributed across the country’s regulatory geographies — Baddi in Himachal Pradesh for the excise-legacy formulation lines, Ahmedabad-Vadodara and Halol in Gujarat for finished dosage forms and biosimilars, Bachupally and Bollaram in the Hyderabad-Vishakhapatnam corridor for API and formulation blocks, and a research and development site in the Ahmedabad-Vadodara belt. Torrent Pharmaceuticals operating as the reference brand persona for this article runs an integrated finance function with a central tax cell in Ahmedabad, plant-level tax coordinators at each site, and quarterly reporting to a board audit committee that reviews signed statutory audit sign-off from the engagement partner.
Torrent Pharmaceuticals is one Tier-1 example — the same operating pattern applies to Sun Pharmaceutical Industries with its Halol and Ahmedabad plants and its Mumbai-Thane corporate office, to Dr Reddy’s Laboratories with its Hyderabad plant network and Bachupally research site, to Cipla with its Mumbai and Kurkumbh plants, to Lupin with its Ankleshwar and Ahmedabad-Vadodara plants, and to Zydus Lifesciences with its Ahmedabad and Ankleshwar network. The relevant reading discipline for the Council FAQ is identical across the Tier-1 formulator group because the underlying HSN classification profile — HSN Chapter 30 formulations, HSN 9018-9022 medical devices where the company also runs a medical-device SBU, and the life-saving drugs schedule where the company holds cancer, HIV, tuberculosis or rare-disease product registrations — determines the exposure surface rather than any one company’s operating footprint.
A pure-play biosimilar or complex-generic player such as Biocon Biologics (the Biocon subsidiary) may see Q51 as the dominant exposure question because its portfolio concentration is in cancer biosimilars that are candidates for the nil-rate schedule. A pure-play API specialist such as Divi’s Laboratories or Laurus Labs may see Q10 as the dominant question because the API business at HSN Chapter 29 sits on the input side of the formulation inversion cascade. A medical-device player such as Poly Medicure or HLL Lifecare reads Q25 as the dominant question because the entire product line is under HSN 9018-9022. The three FAQ questions are therefore not equally weighted across the Indian pharma sector — but the reading discipline that translates each into an ERP-field change and a monthly review cadence is the same.
The regulatory overlay — Section 54(3), Rules 42 and 43, and the amended Rule 89(5)
Three regulatory anchors govern the Council FAQ reading discipline, and each maps to a specific ERP field.
Section 54(3) of the CGST Act 2017 permits a registered person to claim a refund of unutilised input tax credit where the credit has accumulated on account of the rate of tax on inputs being higher than the rate of tax on output supplies — the inverted duty structure. The Supreme Court in Union of India v. VKC Footsteps India Pvt Ltd (2021) 10 SCC 674 upheld the statutory framework and confirmed that the refund is confined to unutilised credit on inputs; input services and capital goods are excluded. Rule 89(5) of the CGST Rules 2017, as amended by Notification 14/2022-Central Tax dated 5 July 2022, provides the operational formula — Maximum Refund Amount = (Turnover of inverted-rated supply × Net ITC / Adjusted Total Turnover) minus (Tax payable on such inverted-rated supply × Net ITC / ITC availed on inputs and input services), where Net ITC excludes input services and capital goods. Q10 of the 56th Council FAQ tells the pharma controller that the inversion structurally deepens after 22 September 2025 because the formulation output rate has dropped to 5 percent flat while the API input rate at HSN Chapter 29 and the packaging input rate at HSN Chapter 39 or 48 continue at 12 percent or 18 percent. The refund pipeline is therefore larger post-cutover and the RFD-01 monthly filing discipline is what keeps that pipeline flowing rather than clogging.
Rule 42 and Rule 43 of the CGST Rules 2017 govern the common-credit reversal where a registered person supplies both taxable and exempt outputs. Rule 42 apportions in-period input and input-service ITC on shared inputs, reversing the exempt-attributable portion in the same tax period. Rule 43 apportions capital-goods ITC over a 60-month useful life, reversing the exempt-attributable portion month by month over the amortisation window. Q51 of the 56th Council FAQ clarifies that a nil-rated supply is treated as an exempt supply for the purpose of common-credit apportionment — the specified schedule of life-saving drugs for cancer, HIV, tuberculosis and rare diseases therefore triggers Rule 42/43 obligation the moment the first nil-rate invoice is raised. The ERP-field change is a per-batch attribution flag on the manufacturing register (taxable versus nil), a common-input register for shared inputs, and a monthly Rule 42 apportionment plus a Rule 43 60-month amortisation register.
The DPCO 2013 read with the NPPA ceiling-price notifications provides the third overlay. Q25 of the 56th Council FAQ addresses medical devices under HSN 9018-9022 — the rate reduction from 18 percent to 5 percent alters the tax incidence on the SKU and therefore alters the correct MRP. NPPA under DPCO 2013 Para 20 treats a mismatch between declared MRP and rate incidence as an overcharging exposure with recovery plus interest. The controller’s ERP action is a per-SKU MRP recalculation driven by the price-master file, an inventory-on-hand pause during physical re-labelling of stock at plant and depot, and an audit-trail entry linking the recalculated MRP to the invoice line that first carries the new 5 percent rate.
A worked example — Council FAQ one-pager register at monthly close
Illustrative — the following register represents the operating pattern of a Tier-1 Indian pharma formulator of the scale relevant to the persona. Public disclosures do not reveal per-SKU MRP recalculation status or per-plant Rule 42 apportionment ratios; cross-verify against your own price-master and manufacturing-register extract before action.
The controller’s Council FAQ one-pager register at October 2025 monthly close, for the September-October 2025 straddle period, carries three rows:
| Q | Subject | ERP-field change | Cadence | Exception path |
|---|---|---|---|---|
| Q10 | Deepened inversion plus expedited Section 54(3) refund | RFD-01 filing cycle switched from rolling-quarterly to monthly. Net ITC numerator draws only from inputs; input-services and capital-goods ledgers separated at source | Monthly RFD-01 first two cycles, quarterly board sign-off | Any refund partly disallowed at proper-officer stage flagged to tax head for representation |
| Q25 | Medical device HSN 9018-9022 MRP recalculation | Per-SKU MRP recalculated in price master; inventory-on-hand pause during physical re-labelling at plant and depot; audit-trail entry linking recalculated MRP to first invoice at new rate | Weekly until complete, then monthly reconciliation of re-labelling status | Any SKU invoiced at the new rate before re-labelling completes flagged as DPCO Para 20 exposure |
| Q51 | Life-saving drugs nil rate plus Rule 42/43 reversal | Per-batch attribution flag on manufacturing register (taxable versus nil); common-input register separated from fully-attributed input register; monthly Rule 42 apportionment and Rule 43 60-month amortisation | Monthly Rule 42, quarterly Rule 43 review, annual capital-goods deployment review | Any batch produced on a nil-rate line without attribution flag flagged as Rule 42 apportionment miss |
The illustrative rate impact on the formulator’s monthly output register for October 2025 (first full month post-cutover) shows the pattern the three FAQ answers combine to produce:
| Output line | HSN | Value (Rs crore) | Pre-cutover rate | Post-cutover rate | Post-cutover GST (Rs crore) |
|---|---|---|---|---|---|
| Formulations — general | 3004 | 480.0 | 12 percent | 5 percent | 24.0 |
| Formulations — dressings and pharmaceutical goods | 3005/3006 | 65.0 | 12 percent | 5 percent | 3.25 |
| Medical devices — instruments and apparatus | 9018-9022 | 42.0 | 18 percent | 5 percent | 2.1 |
| Life-saving drugs — cancer, HIV, TB, rare disease | 3004 (scheduled) | 78.0 | 5 percent | Nil | 0.0 |
| Aggregate output GST | 665.0 | 29.35 |
Against this output register, the input side continues to carry 12 percent or 18 percent GST on APIs at HSN Chapter 29, on packaging at HSN Chapters 39 and 48, and on solvents and reagents at HSN Chapter 27 (with the Notification 09/2022-CT (Rate) Section 54(3) block still active for the Chapter 27 solvent leg — see the Rule 89(5) inverted-duty refund for pharma formulations complete guide walkthrough for the solvent-blocked mechanic and the edible-oil Chapter 15 refund blocked article for the same Notification 09/2022 mechanic applied to a different chapter). The Rule 42 apportionment for October produces a nil-rate turnover ratio of 78.0 / 665.0 = 11.7 percent, and the shared-input ITC pool is reversed in that ratio for the tax period.
Common reconciliation breakages
Five breakages recur across Tier-1 Indian pharma formulators translating the 56th Council FAQ into operating practice, and each maps to a specific control failure.
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RFD-01 filing cycle left at rolling-quarterly cadence. Controllers that read Q10 as reference commentary rather than as an instruction leave the pre-cutover quarterly filing cycle in place after 22 September 2025. The refund pipeline then swells because the input-output gap has widened, working capital is tied up in unclaimed ITC, and the first Section 54(3) refund audit at the proper-officer stage flags the delay as a compliance gap. The discipline is to switch to monthly RFD-01 filing for the first two cycles and to review sign-off at the quarterly board meeting.
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Per-SKU MRP recalculation lagging invoice at new rate. Q25 requires MRP recalculation and physical re-labelling before the next taxable invoice at the new 5 percent rate. Where the price-master file update lags the invoice run — the invoice goes out at 5 percent tax against an SKU still carrying the pre-cutover higher MRP — NPPA under DPCO 2013 Para 20 treats the difference as an overcharging exposure recoverable with interest. The discipline is an inventory-on-hand pause on the SKU during re-labelling, with the invoice release blocked until the re-labelling status flag flips.
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Batch-level taxable-versus-nil attribution flag not live before first nil-rate invoice. Q51 requires that shared inputs consumed on nil-rate batches are apportioned under Rule 42 with the exempt-attributable portion reversed in the same tax period. Where the manufacturing register is not carrying a per-batch attribution flag before the first nil-rate invoice, the shared-input consumption is under-attributed to the exempt leg and the Rule 42 reversal is short. The exposure is a Section 74 penalty at year-end audit on the excess ITC claim.
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Net ITC numerator including input services and capital goods. The Rule 89(5) amended formula excludes input services and capital goods from the Net ITC numerator. Some controllers continue to include freight, plant maintenance service, or capitalised plant and machinery ITC in the numerator, and the refund claim is then either partly disallowed at the proper-officer stage or triggers post-audit reversal with interest. The discipline is to separate the input-services ledger and the capital-goods ledger from the raw-material and packaging ledger at source, so the Net ITC ratio in the refund formula draws only from the eligible base.
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Board audit committee reviewing raw FAQ text rather than one-pagers. The three FAQ answers as raw CBIC text are not audit-committee reading material. Where the finance function has not prepared a Council FAQ-anchored one-pager per Q with the ERP-field change, the cadence, and the exception path, the audit committee’s sign-off is against unstructured commentary and the statutory auditor at year-end has to reconstruct the mapping from ERP change logs and change-request tickets. The discipline is a three-row one-pager register maintained by the tax cell, refreshed monthly for the first two cycles and quarterly thereafter, with the statutory auditor invited to the first two cycles as observer.
How a reconciliation platform handles this
A purpose-built pharma reconciliation platform ingests the SKU master and the price-master file, the manufacturing register with the per-batch taxable-versus-nil attribution flag, the common-input register with shared-input consumption per batch, the RFD-01 monthly filing workbook keyed to the amended Rule 89(5) formula, and the DPCO 2013 register linking each scheduled formulation to the NPPA ceiling price and the MRP recalculated for the post-cutover rate. The platform produces the three Council FAQ one-pagers automatically at every month-end close — Q10 with the RFD-01 filing draft under the amended formula and the input-services plus capital-goods exclusion audit trail, Q25 with the per-SKU MRP recalculation completion status and the DPCO Para 20 exception log, and Q51 with the Rule 42 monthly apportionment for shared inputs and the Rule 43 quarterly capital-goods amortisation. The platform surfaces the exception paths as blocking flags on the invoice release rather than as commentary in a review meeting minute. Match rate improvement of 51 to 88 percent on the input-to-output reconciliation chain, combined with an ISO 27001:2022 posture and DPDP Act 2023 aligned data handling, makes the platform an infrastructure investment for a Tier-1 pharma finance function rather than a spreadsheet substitute for the tax cell.
Cross-cluster bridges and where to read next
The Council FAQ reading discipline in this article sets up the entire pharma launch-wave cluster. For the full text of the 22 September 2025 rate transition and the SKU-level cutover mechanics, read the 56th GST Council pharma drugs and medical devices 5 percent transition walkthrough. For the medical-device MRP recalculation workflow at SKU granularity, read the medical device HSN 9018-9022 rate change from 18 to 5 percent article. For the specified nil-rate schedule and the Rule 42/43 apportionment mechanic, read the life-saving drugs at nil rate GST for cancer, HIV, TB and rare disease article. The single most consequential refund cycle for a pharma formulator — the inverted-duty refund on 5 percent formulations against 12 or 18 percent inputs — is unpacked in the Rule 89(5) inverted-duty refund for pharma formulations complete guide, and the same Notification 14/2022 amended formula applied to the dairy sector sits in Dairy inverted-duty refund under Rule 89(5) post GST 2.0 for a cross-cluster reference. For the underlying reconciliation methodology, the reconciliation playbook monthly close cornerstone sets out the cadence discipline that the Council FAQ one-pager register plugs into. The commercial pillar for the pharma sub-cluster is pharma reconciliation software India; the broader authority is reconciliation software India.
The five FAQs below address the operational questions Indian pharma finance controllers ask most often when translating the 56th Council FAQ into ERP-field changes and monthly review cadence.
- ▸ 56th GST Council press release, 3 September 2025 (effective 22 September 2025) — Rate rationalisation for the pharma sector — all drugs and medicaments under HSN Chapter 30 moved to a flat 5 percent output rate; medical instruments and apparatus under HSN 9018-9022 moved from 18 percent to 5 percent; a specified schedule of life-saving drugs for cancer, HIV, tuberculosis and rare diseases moved to a nil rate. The CBIC FAQ accompanying the Council decision publishes Q10 (deepened inversion for formulators plus expedited Section 54(3) refund pledge), Q25 (medical-device HSN 9018-9022 transition mechanics including MRP recalculation and re-labelling) and Q51 (life-saving drugs nil-rate schedule and Rule 42/43 common-credit reversal obligation).
- ▸ Section 54(3), Central Goods and Services Tax Act 2017 — Refund of unutilised input tax credit. Where the credit has accumulated on account of the rate of tax on inputs being higher than the rate of tax on output supplies (the inverted duty structure), a registered person may claim refund of unutilised ITC at the end of any tax period. The Supreme Court in Union of India v. VKC Footsteps India Pvt Ltd (2021) 10 SCC 674 confirmed that the refund is confined to unutilised credit on inputs; input services and capital goods stand excluded.
- ▸ Rule 89(5), CGST Rules 2017, as amended by Notification 14/2022-Central Tax dated 5 July 2022 — Refund formula for the inverted duty structure. Maximum Refund Amount = (Turnover of inverted-rated supply of goods and services × Net ITC / Adjusted Total Turnover) minus (Tax payable on such inverted-rated supply × Net ITC / ITC availed on inputs and input services). The 5 July 2022 amendment applies prospectively — refund applications filed on or after 5 July 2022 use the amended formula, and Net ITC excludes input services and capital goods.
- ▸ Rule 42 and Rule 43, CGST Rules 2017 — Common-credit reversal for taxable plus exempt supplies. Rule 42 governs the apportionment of input and input-service ITC where the registered person supplies both taxable and exempt outputs; the exempt-attributable portion is reversed in the tax period. Rule 43 governs the same apportionment for capital-goods ITC over the useful life of the asset. A pharma formulator producing both taxable formulations at 5 percent and life-saving formulations at nil rate falls squarely within Rule 42/43 because nil-rated supply is treated as exempt supply for the purpose of common-credit apportionment.
- ▸ HSN Chapter 30 (Pharmaceutical products) and HSN 9018-9022 (Medical instruments and apparatus), CGST rate notifications post-22 September 2025 — Rate structure for the pharma sector after the 56th Council rate rationalisation. HSN Chapter 30 formulations (finished dosage forms under HSN 3004, bulk drugs and mixtures under HSN 3003, medicaments in measured doses under HSN 3004, dressings under HSN 3005, and pharmaceutical goods under HSN 3006) all move to a flat 5 percent output rate. HSN 9018-9022 medical instruments and apparatus, dental instruments, X-ray apparatus, and electro-diagnostic apparatus move from 18 percent to 5 percent. A specified schedule of life-saving drugs for cancer, HIV, tuberculosis and rare diseases moves to a nil rate, with the schedule notified in the accompanying rate notification.