When a limited company misses its filing deadlines, penalties arrive from two different directions simultaneously. HMRC fines you for the late CT600 corporation tax return. Companies House fines you for the late annual accounts. The two systems operate independently — you can be penalised by both at the same time, for the same accounting period.
Ignore them long enough and Companies House can strike your company off the register entirely — which has serious consequences for directors and any assets the company holds.
HMRC Penalties: The CT600 Corporation Tax Return
Your CT600 is due 12 months after the end of your company's accounting period. Corporation tax itself must be paid nine months and one day after the period end — before the return is even due. HMRC charges separate penalties for late filing of the return, regardless of whether the tax was paid on time.
HMRC CT600 late filing penalties
| How late | Penalty |
|---|---|
| Up to 3 months | £100 flat penalty |
| 3 to 6 months | £200 flat penalty (in addition to the £100) |
| Over 6 months | 10% of the unpaid corporation tax |
| Over 12 months | A further 10% of the unpaid tax |
If your company has been late for three or more consecutive accounting periods, the flat rate penalties double: £200 for up to three months late, £400 for three to six months late.
The tax interest penalty is separate
In addition to the filing penalties above, HMRC charges late payment interest on any corporation tax not paid by the nine-month deadline. This compounds daily and cannot be appealed — only reduced by paying the underlying tax.
Companies House Penalties: Late Annual Accounts
Separately from HMRC, Companies House requires your annual accounts to be filed within nine months of your accounting period end (for private companies). If you miss this deadline, automatic penalties apply — and unlike HMRC penalties, Companies House fines are fixed regardless of your tax liability.
Companies House late filing penalties
| How late | Private company penalty | Public company penalty |
|---|---|---|
| Up to 1 month | £150 | £750 |
| 1 to 3 months | £375 | £1,500 |
| 3 to 6 months | £750 | £3,000 |
| More than 6 months | £1,500 | £7,500 |
These penalties double if your company was late in the previous year as well. A company that is late two years running with accounts filed more than six months late faces a £3,000 Companies House penalty — plus HMRC penalties on top.
The Bigger Risk: Company Strike-Off
Companies House does not just fine companies for late filing — it can remove them from the register entirely. If accounts remain unfiled for long enough, Companies House issues a strike-off notice and eventually dissolves the company.
When a company is struck off, all its assets — including any money in its bank accounts — pass to the Crown. Directors lose access to company funds immediately. Any personal guarantees on company debts may crystallise. Contracts and leases held in the company name become void. And the company name becomes available for anyone else to register.
Striking off does not eliminate tax debts
HMRC can pursue the directors of a struck-off company personally for unpaid corporation tax, VAT, PAYE, and penalties in some circumstances — particularly where there is evidence of deliberate non-compliance. Dissolution does not make the liability disappear.
How to Fix a Late Company Return
The process for resolving late company filings differs from individual Self Assessment. You typically need to file accounts with Companies House and a CT600 with HMRC simultaneously, ensuring the figures are consistent between the two. If your company has a complex structure, director loans, or property assets, the calculations require professional preparation.
If your company is already subject to a strike-off notice, the filing must happen before the notice takes effect — or you may need to separately apply for restoration, which is a court process.
- 1Establish the accounting period end date for each outstanding year.
- 2Prepare company accounts — profit and loss, balance sheet, and any required notes.
- 3File accounts at Companies House to stop penalty escalation and prevent strike-off.
- 4Prepare and file the CT600 with HMRC using the same accounting figures.
- 5Pay any outstanding corporation tax plus interest, or arrange a Time to Pay plan.
- 6Submit penalty appeals to HMRC where genuine reasonable excuse grounds exist.
Is your Ltd company at risk of being struck off?
Connect with a corporate tax specialist immediately. We handle late CT600s, Companies House filings, and can tell you whether a strike-off notice is already in progress — and how to stop it.