I have recently been having to deal with clients late payment and submission penalties for payroll schemes which ceased last year. Although final declarations were sent HMRC seem to be ignoring them!
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I have had this and a phone call sorted. There was a small reason on mine BUT they of course dont tell you that. Just slam out fines.
Is it a fine or a HMRC assessed estimate of unpaid PAYE?
I had this problem, with a company I inherited the administration of. Despite filing the returns (they were late) I did speak to HMRC when I found assessments had been raised, but the company's records were not updated at their end.
In the end we got a call from a lady from their debt recovery team wanting to come out to discuss paying the 'debt' of circa £700. I explained that there was no liability and the company had no employees and I had submitted the paperwork (online forms) to shut the PAYE scheme down, then a week later, the company were no longer registered for PAYE when I logged in to file their tax return.
Not an ideal situation, but the correct position of no liabilities and no PAYE scheme needed is now showing.