Million face £100 late filing fine
But more than nine out of 10 people met the deadline, the highest proportion since the revenue body was created in 2005.
A record 9.45 million self-assessment tax returns were filed on time this year, meaning 90.4% of taxpayers met the deadline.
The original online filing deadline of January 31 was extended to February 2 because of a strike by tax office staff. The proportion of people who filed online this year rose to 80%, also a record high, and up from the 78% of taxpayers who used the internet last year.
"HMRC have always been clear that they want returns not penalties, so it is good news that over 90% of all returns were submitted on time."
Under the revenue body's new penalty system, those who miss the deadline face an initial £100 fixed penalty, even if there is no tax to pay or if the tax due is paid on time, and additional daily charges of £10 will accrue after three months. A maximum penalty of £1,600 could eventually be due.
The busiest day for online returns was January 31, when HMRC received nearly 445,000.
The "self-assessment rush hour" occurred between 4pm and 5pm on that day, when 37,460 returns, equating to more than one every six seconds, were received.
Some 1,100 people filed online on Christmas Day last year and 11,648 used the internet to do this on New Year's Eve.
© 2012 Press Association