Eighty-eight per cent of 2007-08 tax returns were received on time, according to HMRC statistics.
Around 5.8 million were filed online by the 31 January 2009 deadline.
The Revenue data shows that about 1.3 million returns were not received.
An spokesperson for the department said that HMRC have issued penalties in respect of the late and outstanding returns, broken down as follows:
- 134,958 in respect of online returns filed late;
- 224,529 in respect of late filed paper returns; and
- the balance relates to returns not yet received.