Companies House Late Filing Penalty, CIS & VAT Fines Explained (2026 Guide)

Companies House issued 297,682 late filing penalties in 2024/25, totalling £157.2 million — and unlike HMRC penalties, these can’t be appealed just because you have a reasonable excuse like illness. Many company directors don’t realise Companies House and HMRC are two entirely separate regulators, each with their own filing deadlines, their own penalty structure, and their own — very different — appeal rules.

This guide focuses on the business side of late filing: Companies House accounts penalties, Corporation Tax, VAT, and CIS — what triggers each one, the real current figures, and how the “second-year doubling rule” catches out more companies than almost anything else. If you’re looking for personal Self Assessment deadlines and penalties specifically, see our full HMRC Penalties guide.

Key Takeaways

• Companies House and HMRC are separate regulators — a late accounts penalty from one doesn’t replace a late Corporation Tax penalty from the other; both can apply to the same company in the same year.
• Private company accounts penalties: £150 (up to 1 month late), £375 (1–3 months), £750 (3–6 months), £1,500 (over 6 months).
• These penalties automatically double if you file late in two consecutive financial years — up to £3,000 for private companies.
• Companies House penalties generally can’t be appealed just for a “reasonable excuse” like illness — only genuinely exceptional, unforeseen circumstances are considered.
• VAT uses a points-based penalty system; CIS returns require a monthly nil return even with no subcontractor payments.
• Companies House confirmed in January 2026 that planned digital filing reforms originally due April 2027 have been paused, with no new date set.

Table of Contents

• Companies House vs HMRC: Two Separate Penalty Regimes
• Companies House Late Filing Penalties for Accounts
• The Second-Year Doubling Rule
• Corporation Tax Late Filing Penalties
• VAT Late Filing: The Points-Based System
• CIS Late Filing Penalties
• Penalty Comparison Table
• Appealing a Companies House Penalty (Different Rules)
• 2027 Digital Filing Reform: Paused
• Avoiding Company Late Filing Penalties
• How Much Does Compliance Support Cost?
• Common Mistakes to Avoid
• FAQs
• Sources
• About the Author

Companies House vs HMRC: Two Separate Penalty Regimes

This is the single most misunderstood point for company directors: Companies House and HMRC are entirely separate government bodies with separate filing obligations. Companies House penalises late annual accounts; HMRC separately penalises late Corporation Tax returns (CT600), even though both relate to the same company and often the same year-end. Filing one doesn’t satisfy the other, and missing both means facing two entirely independent sets of penalties.

Accountant Insight: We regularly see directors assume that once their accountant has “done the year-end,” everything is filed. In practice, that year-end work usually produces two separate submissions — to Companies House and to HMRC — on two separate deadlines, and it’s worth confirming both explicitly rather than assuming.

Companies House Late Filing Penalties for Accounts

Private limited companies must deliver annual accounts to Companies House within 9 months of their accounting reference date (year-end) — 21 months from incorporation for a first set of accounts. Missing this triggers an automatic penalty, issued the day after the deadline with no warning:

These penalties are civil fines, not allowable expenses — you can’t offset them against Corporation Tax. Failing to file at all is a criminal offence that can lead to personal prosecution of directors, separate from the financial penalty.

The Second-Year Doubling Rule

If a company files its accounts late for two consecutive financial years, the penalty for the second late year is automatically doubled at every tier — turning a £375 penalty into £750, or the maximum £1,500 into £3,000 for private companies. Filing on time resets you back to the standard penalty band the following year.

Illustrative Example: A company files its 2024 accounts two weeks late and receives the standard £150 penalty. If the same company then files its 2025 accounts three weeks late — still within the same “up to 1 month” band — the penalty doubles to £300, purely because of the previous year’s lateness, not the severity of this year’s delay.

Corporation Tax Late Filing Penalties

Separately from Companies House, HMRC penalises a late CT600 Corporation Tax return as follows:

• 1 day late: £100 fixed penalty
• 3 months late: A further £100 penalty
• 6 months late: HMRC estimates your Corporation Tax bill and adds a 10% surcharge on top
• 12 months late: A further 10% surcharge

Filing late three times in a row increases the flat penalties to £500 and then £1,000 instead of the standard £100 figures. Corporation Tax itself is due for payment 9 months and 1 day after year-end — separate again from the 12-month filing deadline.

VAT Late Filing: The Points-Based System

Since January 2023, VAT late filing uses a points-based system rather than an immediate fine per late return. Each late return earns one point; once you reach your points threshold — generally 2 for annual filers, 4 for quarterly filers, 5 for monthly filers — a £200 penalty applies, with a further £200 for each subsequent late return at or above the threshold. Late payment is penalised separately, with charges that increase the longer the VAT bill stays unpaid, plus interest.

CIS Late Filing Penalties

Contractors must submit CIS returns by the 19th of each month for the previous month’s subcontractor payments. Missing this deadline escalates broadly as follows:

• 1 day late: £100 fixed penalty
• 2 months late: A further £200
• 6 months late: A further £300 or 5% of the deductions on the return, whichever is greater
• 12 months late: A further £300 or 5% of deductions, whichever is greater (rising further for deliberate withholding)

Nil returns — where no subcontractors were paid that month — are still generally required to avoid a penalty. Persistent late filing also risks losing gross payment status, which affects cash flow for the contractor going forward.

Penalty Comparison Table

Appealing a Companies House Penalty (Different Rules)

This is where Companies House differs sharply from HMRC: standard reasons like an accountant’s illness, lack of awareness of the deadline, or “we didn’t know how to file” are generally not accepted. Companies House only considers appeals for genuinely exceptional, unforeseen circumstances outside the company’s control — and unlike HMRC penalties, there’s no tribunal route to escalate a rejected Companies House appeal.

2027 Digital Filing Reform: Paused

Companies House had planned to require fully digital accounts filing, including software-only submission, from April 2027 as part of wider Economic Crime and Corporate Transparency Act reforms. As of January 2026, Companies House confirmed this specific reform has been paused and is under review, with no new implementation date set. 

Avoiding Company Late Filing Penalties

• Register for free Companies House email reminders as soon as your company is incorporated.
• Track your accounting reference date and both the 9-month accounts deadline and 12-month Corporation Tax deadline separately — they’re not the same date.
• Confirm explicitly with your accountant which filings are included in your year-end service, rather than assuming “everything” is covered.
• File CIS nil returns every month you have no subcontractor payments, not just months with activity.
• Monitor VAT points if you’re a quarterly filer — four late returns is easier to reach than it sounds.

Accountant Insight: A single missed deadline rarely sinks a company financially, but the second-year doubling rule means the real damage often comes from a second late filing the following year — building a habit of early filing after any first miss is the highest-value fix.

How Much Does Compliance Support Cost?

Fees for keeping company filings on track typically scale as follows:

Common Mistakes to Avoid

1. Assuming Companies House and HMRC deadlines are the same. They’re separate filings, separate regulators, and separate penalties.
2. Assuming an accountant is fully responsible if a deadline is missed. Legal responsibility for filing sits with the director, even when an accountant prepares the return.
3. Not tracking the second-year doubling rule. A minor delay the year after a first late filing costs double, regardless of how small the lateness is.
4. Missing CIS nil returns. A month with no subcontractor payments still generally needs a nil return.
5. Assuming Companies House will accept the same reasonable-excuse evidence HMRC does. The bar for a successful Companies House appeal is considerably higher.
6. Not checking VAT points regularly. Points can accumulate silently across several quarters before the £200 penalty triggers.

Frequently Asked Questions

Are Companies House and HMRC penalties the same thing?
No. They’re separate regulators with separate filing obligations — a late Companies House accounts penalty and a late HMRC Corporation Tax penalty can both apply to the same company in the same year.

How much is the Companies House late filing penalty?
£150 for up to 1 month late, £375 for 1–3 months, £750 for 3–6 months, and £1,500 for more than 6 months late for a private company — doubling if you’re late two years running.

Can I appeal a Companies House penalty because my accountant was ill?
Generally no. Companies House only accepts genuinely exceptional, unforeseen circumstances — standard reasonable-excuse evidence accepted by HMRC often isn’t accepted here.

Do I still need to file a CIS return if I paid no subcontractors that month?
Generally yes — a nil return is usually still required to avoid a penalty.

How does the VAT points system work?
You get a point for each late return. Once you reach your threshold (based on how often you file), a £200 penalty applies, with a further £200 for each additional late return at or above that threshold.

Is the Companies House digital filing requirement from 2027 still happening?
As of January 2026, this specific reform was paused with no new date confirmed — check Companies House’s current guidance before assuming a fixed timeline.

What’s the maximum Companies House penalty for a private company?
£1,500 for a single late year, rising to £3,000 if you’re late two consecutive years running.

Sources & References

• GOV.UK / Companies House — Late filing penalties
• GOV.UK — Corporation Tax penalties
• GOV.UK — VAT penalty points and penalties
• GOV.UK — CIS contractor obligations and penalties
• GOV.UK — Annual accounts and Companies House filing

Conclusion

The single biggest risk for company directors isn’t any one penalty — it’s confusing Companies House and HMRC as if they’re the same obligation, or assuming a Companies House penalty can be appealed as easily as an HMRC one. Track both deadlines separately, file early enough to build a buffer, and treat any first late filing as a warning to never repeat it, given how the second-year doubling rule works.

Need help staying ahead of your Companies House, Corporation Tax, VAT or CIS deadlines? Call 0116 4030595, email info@taxreturnaccountants.uk, or get in touch for a free consultation.