CA K Sanjay BhargavChartered Accountant
Open menu

Manufacturing Taxation: GST, Credit and Compliance

A manufacturer’s tax problems are almost never about the monthly return. They are about credit that does not come back and tests that are failed silently — and they share one uncomfortable feature.

Nothing in your monthly filing discloses any of them. The MSME payment position is fixed on 31 March. Goods with a job worker age against a clock nobody is watching. Credit distributed by the wrong mechanism across states is never flagged. Refund periods go out of time without a prompt. By the time the annual reconciliation finds them, most are no longer fixable.

Who this is for

  • Factories and industrial units — engineering, fabrication, auto components, electronics, plastics, food processing, textiles.
  • MSMEs, both as suppliers and as buyers from other MSMEs.
  • Multi-state operations with more than one GST registration under a single PAN.
  • New plants in the capex phase, where the credit position is decided rather than discovered.

The dates and tests that nothing reminds you about

WhatWhen it is decidedWhat a monthly return tells you
MSME payment ruleFixed at 31 March — no relief for paying laterNothing
Job work return period1 year (inputs) / 3 years (capital goods) from despatchNothing until the deemed supply has already arisen
Inverted duty refundLimitation runs from a relevant date, oldest firstNothing
ISD distributionMonthly, but a wrong allocation is silentNothing
Factory capex creditAt contracting and capitalisationNothing — and it is unfixable afterwards

That column of “nothing” is the whole argument for looking at these on a cycle rather than at year end.

⚠️ The 31 March cliff

Deductions allowed on payment normally carry a forgiving rule: pay before the due date for filing the return and the deduction survives in the year it was incurred. For micro and small enterprises that relief does not apply.

An amount outstanding beyond the permitted window at 31 March is disallowed for that year and allowed only when paid. There is no remedial payment and no filing-date rescue. On 1 April the position is fixed.

The window is 45 days with a written agreement and 15 days without one — and businesses assuming 45 days frequently do not have the agreement that would give it to them. It reaches micro and small only; medium enterprises and traders are generally outside it, so indiscriminate provisioning overstates the exposure as often as ignoring it understates it. See the MSME 45-day rule.

Credit that does not come back

Three separate leaks, with different causes:

  • Factory construction. Credit on constructing immovable property on your own account is blocked. The functional-plant route opened by Safari Retreats was closed by a retrospective amendment to 1 July 2017. What survives is credit on plant and machinery — so the value now sits at the boundary, and the boundary is set by how contracts are split and how assets are capitalised during capex, not afterwards.
  • Inverted duty. Where inputs are taxed above your output, credit accumulates. The refund covers inputs only — not input services or capital goods — and the formula apportions by turnover, so the recovery is structurally smaller than the balance. The residue is often permanent, which makes it a pricing and balance-sheet question rather than only a refund one.
  • Multi-state distribution. Credit taken by the wrong registration is wrongly taken, whatever the group position, and it accumulates without ever being flagged.

Job work — an ageing problem, not a filing one

Goods sent to a job worker move on a delivery challan without tax, and that is not a supply — provided they come back in time: one year for inputs, three for capital goods, with tooling treated separately.

Miss it and the supply is deemed to have occurred on the date of despatch. The consequence is entirely backdated: tax as of that date, and interest running from then rather than from when the lapse was noticed. A consignment sent in April and found missing eighteen months later carries eighteen months of interest.

Separately, the rate on the job worker’s own invoice changed on 22 September 2025 — and for general engineering, fabrication, auto parts, electronics assembly and plastics it went up, from 12% to 18%. See job work: challans, time limits and rates.

Scrap — the obligations sit with the buyer

From 10 October 2024, a registered buyer of metal scrap pays GST under reverse charge where the supplier is unregistered, and deducts 2% GST TDS where the supplier is registered and the contract crosses the threshold.

Both landed on the purchaser, which is not where a manufacturer who thinks of itself as a scrap seller looks. Buying from unregistered yards also affects your registration position, because reverse-charge liability requires registration and the turnover threshold does not shelter it.

The corporate rate election

Worth stating plainly because a great deal of published material has not caught up: the 15% concessional rate for new manufacturing companies has lapsed. It required manufacturing to commence by 31 March 2024 and was never extended, so it is closed to new entrants — though companies that qualified and opted in continue.

The realistic comparison for a new plant is now the general 22% regime. That election is irrevocable for subsequent years and is conditional on forgoing specified deductions, so a company with substantial unabsorbed depreciation can be worse off under the lower headline rate. It has to be modelled on projected numbers before it is made. See is the 15% rate still available?

What to send

  • Creditor ledger with supplier Udyam status and category — micro, small or medium, and manufacturer, service provider or trader
  • Ageing of goods lying with job workers, by despatch date
  • Credit ledger and your input/output rate profile, if credit is accumulating
  • The list of GST registrations under your PAN, and how common costs are currently allocated
  • For a plant under construction, the capex schedule with contractor invoices and how each asset is being capitalised

The last one is the only item on this page where timing is genuinely one-way: the credit position on a new plant is decided while the contracts are being written, and reconstructing a split from a composite works contract afterwards is much weaker. Where a notice has already been issued, see tax notices and assessments.

Frequently asked questions

Why do these problems always surface late?

Because almost none of them appear in a monthly return. The MSME payment position is tested across a financial year and is fixed on 31 March. Goods lying with a job worker age quietly against a one or three year clock. Credit distributed by the wrong mechanism across states is never flagged. Refund periods go out of time without any prompt. Monthly filing is designed to report what happened, not to warn you about a test you are failing, so a manufacturer that only reconciles at year end learns about all of these at the point when none of them can still be fixed.

Can we claim input tax credit on constructing our factory building?

Generally no. Credit on goods and services used for construction of immovable property on your own account is blocked, and the route that briefly opened — treating a functionally essential building as plant after the Supreme Court's decision in Safari Retreats — was closed by a retrospective amendment substituting 'plant and machinery' for 'plant or machinery' with effect from 1 July 2017. Credit on the plant and machinery itself is unaffected. The money now sits at the boundary between the two, and that boundary is decided by how contracts are split and how assets are capitalised during the capex itself.

We buy from MSME suppliers. What is our exposure at 31 March?

Any amount outstanding to a micro or small enterprise beyond the permitted window at 31 March is disallowed for that year, and the usual relief of paying before the return due date expressly does not apply. That makes 31 March final rather than a soft date. The window is 45 days where there is a written agreement and 15 days where there is not, which catches businesses assuming 45 days without having the agreement that would give it to them. Medium enterprises and traders are generally outside it, so over-provisioning is as common as under-provisioning.

We have accumulated credit from an inverted duty structure. How much comes back?

Less than the ledger balance. The refund reaches credit on inputs only, not input services or capital goods, and the prescribed formula scales it by the ratio of inverted-rated turnover to total turnover, so any non-inverted sales dilute the claim. What remains is often a structural residue that will not be recovered while the rate profile stays as it is — which matters for how it is carried in the accounts and priced into the product, not just for the refund application.

We operate in three states. Has anything changed?

Yes, and many multi-state businesses have not acted on it. Since 1 April 2025, credit on common input services procured centrally must be distributed through an Input Service Distributor registration. Cross-charge is no longer an alternative for that purpose and now covers internally generated services only. Because each registration stands alone, credit taken by the wrong one is wrongly taken even where the group paid the right tax overall, and nothing in the monthly returns flags it.

Running a factory or industrial unit?

Send your creditor ledger with supplier MSME status, the ageing of goods with job workers, and your credit position. What is accumulating quietly and what has a date attached to it are established while both can still be acted on.