The figure of 1.1m is the lowest since online filing first started, and compares with 1.4m last year and 1.6m the year before, reports the BBC.
HM Revenue and Customs allowed an extra two days’ grace beyond the normal 31 January deadline due to strike action.
However, 1.1m people failed to file by the end of 2 February.
They will have to pay the £100 fine unless they have a reasonable excuse.
Valid reasons include serious illness, a bereavement, or a loss of documents because of theft, fire or flood.
After three months, additional fines of £10 a day start to accrue and could eventually amount to a maximum of £1,600.