PAYE underpayments
The RTI computer frequently asks employers to pay amounts of PAYE they don’t owe. These apparent underpayments of PAYE can be generated by mistakes the computer makes, such as misallocating PAYE payments, or ignoring claims for set-off of statutory payments or CIS tax.
The phantom PAYE debt can include a “specified charge”, which is imposed when the computer thinks it is missing an RTI return. The specified charge is not a penalty for non-submission of an RTI return – it is simply an estimated amount of PAYE. The charge should be removed once the missing RTI return is submitted.
If you disagree with an apparent underpayment of PAYE, and you are certain you have submitted all the RTI returns required and paid all the PAYE due on time, the matter needs to be referred to the HMRC Disputed Charges Team, We can help with this. If HMRC’s debt collection arm start demanding payment of the PAYE, telling them this has been done should satisfy them.
The next thing to do is to wait, and wait. HMRC has said that an update on the disputed debt, or possibly even a solution, will be provided within three months of the referral to the disputed charges team. Don’t hold your breath.