It has also extended the deadline for returns by 24 hours, in an effort to allay fears by those who have been unable to file their forms online in time because of the site's problems.
Late payers face a fine. "HMRC takes any disruption of service very seriously and to reflect this no-one who files electronically or by paper by midnight Friday 1 February will face a penalty," it said in statement.
104,000 people had successfully filed their tax returns today, taking the total for this year to 3.6 million, HMRC said.
This morning users attempting to file their returns were met with the message: “We are sorry but the service is currently unavailable ... We apologise for any inconvenience that this may cause.” The site provided a link which promised further information, but only warned of future upgrade work due on 13 and 14 February.
No explanation has yet been offered for the problem, which HMRC is understood to be investigating. The news marks the second HMRC website problem in a week, after it admitted it had barred MPs and celebrities from using the service, insisting they should file their tax returns by post to ensure security.