HMRC said it has fixed errors in its employment records.
The errors affected some employers who employ an individual to do more than one job within the same PAYE scheme, HMRC said. In some instances, separate employments were merged in error.
Before HMRC corrected, employers will have seen incorrect information about payroll tax paid and owed on a part of HMRC's website called the business tax dashboard.
HMRC said the dashboard will "shortly show" corrected figures.
This will mean that:
Employers who have been paying the right amount of tax (based on their payroll) should see their accounts now balance on the dashboard. Prior to the records being updated they will have been in a credit position
Employers who have been paying the amount that the dashboard said that they owed (rather than the amount based on their payroll) may end up in debt when the record is updated