Penalties will apply:
Where a Full Payment Submission (FPS) has not been filed on or before the date you paid your employees, or where you have not revealed why submission is legitimately late by using the late reporting reason field.
Where the expected numbers of submissions have not been received.
These rules apply to each PAYE scheme, rather than each employer.
How do I avoid incurring a late filing penalty?
You must submit an FPS each time you make a payment to an employee, on or before the date that you pay them.
If you don’t need to send an FPS because you did not pay any employees in a tax month, it is important that you inform HMRC by sending a nil Employer Payment Summary (EPS) by the 19th of the following tax month. Otherwise, it is likely that it will be assumed that you have missed a submission and will therefore issue a late filing penalty, which you will have to appeal.
To help get your PAYE up-to-date and avoid future penalties, you should take note of any late and non-filing electronic Generic Notification Service (GNS) warning messages which we send to help you get your PAYE affairs up to date – see the Using HMRC's Online Service - PAYE for employers for more information.