Late Filing of Audit Report Not Fatal if Done During Set-Aside Proceedings.

By | November 6, 2025

Late Filing of Audit Report Not Fatal if Done During Set-Aside Proceedings.


Issue

Can a charitable trust be denied the exemption under Section 11 on the procedural ground of delay in furnishing the audit report, if the said report is filed during “set-aside” (remanded) assessment proceedings?


Facts

  • The assessee-trust, duly registered under Section 12A, was claiming exemption under Section 11.
  • The original assessment was “set aside” and remanded back to the Assessing Officer (AO) for fresh adjudication.
  • During these set-aside proceedings, the assessee-trust filed its return of income along with the required audit report.
  • The AO denied the exemption under Section 11, citing the procedural delay in filing the audit report (i.e., it was not filed with the original return).

Decision

  • The court held that the late filing of an audit report does not automatically disentitle a registered trust from availing the benefits of Section 11.
  • Since the assessee filed the audit report during the set-aside proceedings (which are fresh proceedings), the AO could not deny the exemption on the procedural ground of delay.

Key Takeaways

  • Substance Over Form: The filing of an audit report is a procedural, directory requirement, not a mandatory one that would void the exemption if filed late, as long as it is filed before the assessment is finalized.
  • Set-Aside Proceedings are a Fresh Start: A set-aside proceeding provides the assessee an opportunity to cure procedural defects, including the late filing of required documents like the audit report.

Major Port Trust is a “Local Authority” for Tax Purposes.


Issue

Whether a Port Trust, constituted under the Major Port Trust Act, 1963, and functioning under the control of the Central Government, qualifies as a “local authority” for the purposes of the Income-tax Act.


Facts

  • The assessee, a Port Trust, filed its return identifying as a “local authority” but did not claim the corresponding exemption under Section 10(20).
  • The Assessing Officer (AO) rejected this status and treated the assessee as a “trust.”
  • The Commissioner (Appeals), relying on previous High Court judgments, reversed the AO’s order and held that the assessee was indeed a “local authority.”
  • The assessee was constituted by the Major Port Trust Act, 1963, and functioned under the Ministry of Shipping, Government of India.

Decision

  • The court affirmed the order of the Commissioner (Appeals).
  • It held that the assessee qualifies as a “local authority” by virtue of the General Clauses Act, 1897, and its constitution under a specific Act of Parliament.
  • The revenue failed to bring any new facts on record to distinguish the assessee’s case from the binding judicial precedents.

Key Takeaways

  • Definition of “Local Authority”: Entities constituted by a government under a specific Act (like the Major Port Trust Act) and functioning under government control fit the definition of a “local authority” under Section 3(31) of the General Clauses Act, 1897.
  • Binding Precedent: Tax authorities are bound by the decisions of jurisdictional High Courts on the same issue.

Prior Period Interest Expense Claimed on Switching to Mercantile System is Allowable.


Issue

Can an interest expense pertaining to prior years be validly claimed in the current assessment year, when the claim arises due to a bona fide change in the method of accounting from a cash basis to a mercantile basis for that specific item?


Facts

  • Up to AY 2002-03, the assessee (a PSU) followed a mixed method of accounting: cash basis for interest expenses, mercantile for most other items.
  • From AY 2003-04, it switched to a full mercantile system, including for interest.
  • This change led to the recognition of accrued interest from prior years (approx. ₹892 crores), which was debited to reserves. The assessee claimed this as a deduction.
  • The AO disallowed the claim, arguing it was “prior period expenses” and also invoked Section 14A, as the income in those prior periods was exempt.

Decision

  • The court held that the disallowance was unjustified.
  • Since the interest expenses were never accounted for or claimed in the earlier periods (due to the cash system being followed), they cannot be dismissed as “prior period expenses.”
  • Because the expenses were not claimed in the prior exempt periods, the disallowance under Section 14A is not applicable.

Key Takeaways

  • Change in Accounting Method: A liability that crystallizes in the current year due to a bona fide change in accounting method (from cash to mercantile) is allowable in the year of the change.
  • Not a “Prior Period Expense”: An expense is not a “prior period expense” if it was never recorded or claimed in the prior period’s books as per the accounting method then in force.

Prior Period Expenses Must Be Set Off Against Prior Period Income Taxed in Current Year.


Issue

If an Assessing Officer (AO) taxes income that pertains to a prior period in the current assessment year, are they also obligated to allow a deduction for the expenses related to that same prior period?


Facts

  • The AO, based on the tax audit report, noted that the assessee had “prior period income” of ₹4.27 crores and “prior period expenses” of ₹2.53 crores.
  • The AO added the prior period income to the assessee’s current income.
  • However, the AO did not provide the corresponding benefit (deduction) for the prior period expenses.

Decision

  • The court held that this approach was inconsistent and unjust.
  • It ruled that if prior period income is brought to tax in the current year, the expenses related to that income must also be set off against it. Only the net income can be taxed.
  • The matter was remanded to the AO to allow the set-off, subject to verification that the expenses and income are related.

Key Takeaways

  • Consistency Principle: An AO cannot “cherry-pick” by taxing an income item from a prior period while simultaneously ignoring the related expense item from that same period.
  • Taxation of Net Income: The fundamental principle of taxation is to tax the net income, not just gross receipts, especially when both income and related expenses are from the same “prior period” bucket.

Capital Expenditure is a Valid Application of Income for a Charitable Trust.


Issue

For a charitable trust claiming exemption under Section 11, does capital expenditure qualify as a valid “application of income” for charitable purposes?


Decision

  • The court held that yes, capital expenditure incurred by a trust is to be treated as an “application of income” for the purpose of its charitable objects.

Key Takeaways

  • Application is Not Limited to Revenue Expenses: The term “application of income” for charitable purposes is broad. It includes not only revenue expenses but also capital expenditure (like the purchase of a building or equipment) as long as the asset is used to further the charitable objects of the trust.

Gratuity and Superannuation Fund Payments are a Valid Application of Income.


Issue

Do contributions made by a charitable trust (exempt under Section 11) to a gratuity fund and a superannuation fund for its employees qualify as an “application of income”?


Decision

  • The court held that yes, if the assessee is granted the benefit of Section 11 exemption, then expenditures on account of a gratuity fund and superannuation fund must be allowed as an application of income.

Key Takeaways

  • Employee Welfare as Charitable Application: Expenses related to the welfare of a trust’s employees (who are engaged in carrying out the charitable activities) are considered a valid application of income for the purposes of Section 11.

Income Must Be Taxed in the Year of Accrual Under the Mercantile System (Wharfage).


Issue

Can an assessee following the mercantile system of accounting defer the recognition of accrued income (Wharfage services) to a later assessment year when it is actually received?


Facts

  • The assessee (a Port Trust) provided Wharfage services in the previous year relevant to AY 2003-04.
  • It followed the mercantile system of accounting.
  • However, it offered this income to tax in AY 2005-06.
  • The AO taxed the income in AY 2003-04, the year it accrued.

Decision

  • The court ruled in favour of the revenue.
  • It held that an assessee following the mercantile system must recognize income when it accrues (i.e., when the right to receive it is established).
  • The income for Wharfage services, having accrued in AY 2003-04, was correctly taxed by the AO in that year.

Key Takeaways

  • Mercantile System is Binding: An assessee cannot unilaterally choose to follow a receipt (cash) basis for a specific income item when its regular method of accounting is mercantile.
  • Accrual is the Taxable Event: Under the mercantile system, the taxable event is the accrual of income, not its receipt.

Accrued Environment Monitoring Charge Taxable in Year of Accrual.


Issue

(Same as Case VII) Can an assessee following the mercantile system defer the recognition of an accrued Environment Monitoring charge to the year of receipt?


Facts

  • The assessee offered income from an Environment Monitoring charge in AY 2005-06 (on a receipt basis).
  • The AO held that the income had become due (accrued) in AY 2003-04.
  • The assessee follows the mercantile system.

Decision

  • The court ruled in favour of the revenue.
  • It held that the income, having accrued in the previous year relevant to AY 2003-04, was correctly included as income of that year by the AO.

Key Takeaways

  • (Same as Case VII) The principle of the mercantile system is strictly applied. Income is taxable when the right to receive it is established, not when it is actually received.

Loss on Assets Sold in a Prior Year Cannot Be Claimed in the Current Year.


Issue

Can an assessee claim a capital loss in the current assessment year when the asset was actually sold in a much earlier assessment year?


Facts

  • The assessee claimed a loss in Assessment Year 2004-05 from the sale of a bulk terminal.
  • The AO found that the assets were actually sold in the Financial Year 1999-2000.
  • The AO disallowed the claim for the loss in AY 2004-05.

Decision

  • The court ruled in favour of the revenue.
  • It held that since the assets were sold in FY 1999-2000, the assessee could not claim the resulting loss in Assessment Year 2004-05.

Key Takeaways

  • Sanctity of the Assessment Year: This principle applies to losses just as it does to income. A loss (or gain) must be recognized in the assessment year in which the transaction giving rise to it occurs.
IN THE ITAT PUNE BENCH ‘B’
Deputy Commissioner of Income-tax
v.
Jawaharlal Nehru Port Trust Administrative Building
R.K. PANDA, Vice President
and Ms. Astha Chandra, Judicial Member
IT Appeal Nos.543, 544, 545, 1153, 1154 and 1155 (MUM) of 2016
[Assessment years 2003-04 to 2005-06]
SEPTEMBER  30, 2025