HMRC said the penalty would be in addition to the notice sent out in November for the four months between 7 July and 6 November 2008.
Employers are being urged to file their returns as quickly as possible.
HMRC went on to say that letters of apology have now been sent to all employers who submitted their 2007-08 P11D(b) Return of Class 1A National Insurance contributions on time, but who received an incorrect penalty notice.
The letters explain that the incorrect penalty has been cancelled.
Employers who haven’t received the apology letter but who still think that the penalty is wrong can contact HMRC by calling 0845 7 143 143.