StartupGrants India

Company Compliance Health Check

Identify and resolve compliance gaps before they become penalties

What is Company Compliance Health Check?

A Company Compliance Health Check is a structured review of a company's statutory filings, regulatory obligations, and internal governance records to identify gaps, lapses, and potential penalty exposures. Conducted by qualified professionals, it covers MCA filings, income-tax and GST returns, labour law registrations, and secretarial records under the Companies Act, 2013. The output is an actionable remediation report.

Every company incorporated in India operates under a matrix of statutory and regulatory obligations spread across multiple authorities. The Companies Act, 2013 mandates timely filings with the Registrar of Companies, including annual returns, financial statements, and event-based forms for changes in directors, registered offices, share capital, and charges. Separately, the Income Tax Act, 1961, the Goods and Services Tax framework, and applicable labour laws such as the Employees' Provident Fund and Miscellaneous Provisions Act, 1952, and the Employees' State Insurance Act, 1948, impose their own reporting and deposit obligations. A Company Compliance Health Check is a diagnostic exercise that systematically examines every layer of this obligation matrix to produce a clear picture of where the company stands and what remedial action is required. The need for such a review arises most acutely at specific inflection points: when a company is being prepared for external investment, when it is undergoing a merger or acquisition, when the founders are contemplating a change in structure, or when the company has operated informally and grown faster than its compliance infrastructure. Investors and acquirers conduct their own due diligence, and undisclosed compliance gaps discovered during that process can delay transactions, reduce valuations, or result in liability being attributed to the founders. A proactive health check allows the company to identify and remediate issues before they surface in an adverse context. The review covers several distinct domains. On the Ministry of Corporate Affairs side, the professional examines whether all annual returns in Form MGT-7 or MGT-7A and financial statements in Form AOC-4 have been filed within the prescribed deadlines, whether all event-based filings such as Form DIR-12 for changes in directors, Form PAS-3 for allotments, Form SH-7 for increases in authorised capital, and Form CHG-1 for creation of charges have been completed accurately and within time. Any missed filing triggers additional fees under Section 403 of the Companies Act and potentially prosecution under Section 137 or 92. The income-tax review verifies that all advance tax instalments have been paid on time, that TDS deducted from employee salaries, contractor payments, and rent has been deposited by the applicable due dates, that TDS returns in Forms 24Q and 26Q have been filed, and that the annual income-tax return under the applicable form has been submitted. Lapses in TDS compliance attract interest under Sections 234A, 234B, and 234C and penalties under Section 271C. The GST review covers timely filing of GSTR-1, GSTR-3B, and GSTR-9 annual returns, accurate reconciliation of input tax credit claimed against GSTR-2B, and compliance with e-invoicing obligations where applicable based on the company's aggregate turnover. The review also examines whether the company has obtained all required registrations, including Professional Tax registrations in applicable states, Shop and Establishment Act registrations, and EPF and ESI registrations once the headcount thresholds are crossed. Secretarial compliance, including the maintenance of statutory registers such as the Register of Members, Register of Directors and Key Managerial Personnel, Register of Charges, and minutes books for Board and general meetings, is also examined. Non-maintenance of these registers attracts penalties under the Companies Act. The output of the health check is a structured compliance dashboard listing each obligation, its status, the quantum of penalties already accrued, and the recommended remediation steps. For filings that can still be made under the Companies Fresh Start Scheme or any currently active amnesty window, the report identifies the opportunity and the corresponding reduced fee. For genuinely time-barred lapses, the report advises on compounding or adjudication routes.

Who Needs Company Compliance Health Check?

Startups preparing for a funding round or acquisition, companies that have been primarily focused on operations and have not maintained active compliance oversight, businesses that have undergone changes in directors or shareholding without completing the corresponding MCA filings, and any company that has not conducted an internal compliance review in the preceding twelve months.

What's Included

  • Complete picture of compliance status across all regulatory authorities
  • Quantified penalty exposure enabling informed remediation decisions
  • Reduced risk of regulatory action, prosecution, or company strike-off
  • Investment-readiness report for founders approaching funding rounds
  • Identification of amnesty and compounding windows to minimise penalties
  • Structured remediation roadmap with prioritised action items

⚠️ Penalty for Non-Compliance

Non-filing of annual returns and financial statements with the ROC attracts additional fees of one hundred rupees per day of delay under Section 403 of the Companies Act, 2013, with no upper cap. Persistent defaults can result in prosecution of directors under Sections 92 and 137, and the ROC has powers to strike off the company under Section 248.

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How It Works

  1. 1

    Document collection and intake

    Gather the company's incorporation documents, MCA filing history, financial statements, tax returns, GST records, labour law registrations, and statutory registers for the review period.

  2. 2

    MCA and secretarial review

    Examine all ROC filings for completeness and timeliness, review statutory registers and minutes books, and identify missed event-based forms and annual filings with the corresponding penalty computation.

  3. 3

    Tax compliance review

    Verify income-tax return filings, advance tax payments, TDS deduction and deposit records, TDS return filings, and GST return filings and reconciliations against GSTR-2B.

  4. 4

    Labour law and other regulatory review

    Confirm EPF and ESI registration and timely monthly challan deposits, verify Professional Tax compliance in applicable states, and check Shop and Establishment Act registration status.

  5. 5

    Compliance dashboard and remediation report

    Compile findings into a structured report with each obligation, its status, estimated penalty exposure, and recommended remediation action including available amnesty or compounding routes.

  6. 6

    Remediation support

    Assist with filing overdue forms, computing and paying additional fees, filing compounding applications where applicable, and updating statutory registers to bring the company to full compliance.

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Documents Required

Items marked Required are mandatory; others are situational.

Corporate Documents

  • Certificate of Incorporation and MOA/AOARequired
  • MCA filing history (SRN records)Required
  • Statutory registers and minutes booksRequired

Financial and Tax Records

  • Audited financial statements for past three yearsRequired
  • Income-tax returns and Form 26AS for past three yearsRequired
  • TDS challans and return acknowledgements (Forms 24Q/26Q)Required
  • GST registration certificate and GSTR filing summaryRequired

Labour and Other Registrations

  • EPF and ESI registration certificates and challan recordsRequired
  • Professional Tax registration certificate (applicable states)
  • Shop and Establishment Act registration
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Fees & Pricing

Government Fees

Additional MCA filing fees for delayed forms (if applicable)

Computed at one hundred rupees per day of delay per form under Section 403 of the Companies Act, 2013; varies significantly based on the number and age of defaults

Varies

Compounding fee (if applicable)

Determined by NCLT or Regional Director based on the nature and period of default; assessed case-by-case

Varies

Professional Fees

Compliance health check and remediation report

Quoted on review of your specific case

Varies

* Government fees may vary. GST applicable on professional fees. Final pricing confirmed after review.

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Frequently Asked Questions

What is the difference between a compliance health check and a statutory audit?

A statutory audit under Section 139 of the Companies Act, 2013 is a mandatory annual examination of the company's financial statements by an independent Chartered Accountant, primarily focused on financial accuracy and disclosure. A compliance health check is a broader diagnostic covering regulatory filings across MCA, income-tax, GST, labour law, and secretarial requirements. The two are complementary; the health check often identifies filings that the audit process does not examine.

How far back should the compliance health check review?

The standard review covers the preceding three financial years, which aligns with the typical due diligence window used by investors and acquirers. For companies with longer histories or specific areas of concern, the review period may be extended to five or seven years. The limitation period under the Companies Act, 2013 for prosecution is three years from the date of default for most offences, though there is no limitation on additional fees for delayed filings under Section 403.

What is the penalty for not filing annual returns with the ROC?

Under Section 403 of the Companies Act, 2013, filing a document after the prescribed due date attracts an additional fee of one hundred rupees per day for each day of delay, with no cap on the total accumulation. For annual returns under Section 92, persistent non-filing also exposes the company and its directors to prosecution under Section 92(5), which can result in a fine of up to five lakh rupees and imprisonment of up to six months for officers in default.

Can overdue MCA filings be made now, and will penalties be waived?

Overdue MCA filings can generally be made at any time by paying the applicable additional fees calculated under Section 403, regardless of how old the default is. The Ministry of Corporate Affairs has periodically introduced amnesty schemes such as the Companies Fresh Start Scheme and Scheme for Relaxation of Time that cap or waive additional fees for a limited window. The practitioner will identify whether any such scheme is currently active and advise on the optimal filing strategy during the health check.

What GST obligations does the health check review?

The GST review covers filing status and timeliness of GSTR-1 (outward supply details), GSTR-3B (monthly summary return), and GSTR-9 (annual return) under the Central Goods and Services Tax Act, 2017. It verifies reconciliation of input tax credit claimed against GSTR-2B, checks for any notices received from the GST authority, and confirms compliance with e-invoicing obligations under Rule 48(4) of the CGST Rules for taxpayers above the applicable turnover threshold.

Does the health check cover labour law compliance?

Yes. The health check covers registration and monthly deposit compliance under the Employees' Provident Fund and Miscellaneous Provisions Act, 1952 (applicable when headcount reaches twenty employees) and the Employees' State Insurance Act, 1948 (applicable when headcount reaches ten employees in most states). It also reviews Professional Tax registration in states such as Maharashtra, Karnataka, Tamil Nadu, and West Bengal, and Shop and Establishment Act registration in the applicable state.

How is the compliance health check output delivered?

The output is a structured written report typically organised as a compliance dashboard with colour-coded status indicators (compliant, delayed but remediable, penalty-accrued, critical) for each obligation, followed by a narrative section explaining the findings and a prioritised remediation roadmap. The report quantifies the estimated penalty exposure as of the date of the review and identifies the remediation steps required to achieve full compliance, including estimated costs.

Is a compliance health check necessary if the company has an external auditor?

Yes. The statutory auditor's mandate under the Companies Act, 2013 is limited to auditing the financial statements and issuing an audit report. While the auditor's report under CARO (Companies Auditor's Report Order) does address certain compliance matters such as TDS, EPF, and charges, it does not comprehensively review all secretarial filings, event-based forms, GST returns, or labour law registrations. The health check fills that gap and is a broader, purpose-built diagnostic tool.

What is compounding of offences under the Companies Act, and can it help resolve defaults?

Compounding under Section 441 of the Companies Act, 2013 is a process by which a company or its officers pay a sum to the National Company Law Tribunal or the Regional Director in lieu of prosecution for a compoundable offence. Not all offences are compoundable; only those not punishable with imprisonment alone or with both imprisonment and fine are eligible. Compounding resolves the criminal liability for past defaults and is particularly relevant for offences that are beyond the reach of simple additional-fee filings. The health check identifies which defaults are compoundable and assists with preparing the application.

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Company Compliance Health Check

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