Complaints to the Australian Taxation Office have increased by more than 40 per cent in three years, coming amid thousands of job losses and serious IT system failures which saw staff sent home and taxpayers left without key services in December.

The federal opposition has linked the 3347 job cuts by the Turnbull and Abbott governments since July 2014 to the sharp rise in complaint numbers, totalling 34,323 in the 2015-16 financial year. Complaints were across a range of services including form processing, tax return lodgement, superannuation and debt repayment.

Complaints to the Tax Office fell by more than 20 per cent in 2011-12 - from more than 30,000 - after a review of handling processes, and dropped a further 10 per cent a year later.

But since 2013-14 the total number has gone up year on year, increasing by 44 per cent to 2015-16.