The Australian Taxation Office (ATO) will shed 900 jobs over the coming nine months as it searches for budget savings, with most of the job cuts linked to government plans to abolish its controversial mining profits tax.

The ATO said said about half of the 900 jobs would be from natural attrition, and the remainder would be from voluntary redundancies from its 23,000 workers, saving about $50 million this financial year.

While the ATO said it could not say which areas would be affected, it said the abolition of the mining tax could lead to about 200 jobs cut from offices in Perth, Melbourne and Brisbane.

"Our best view is that we need to move our allocations down by about $50 million between now and the end of the financial year," the ATO's Geoff Leeper told a Senate estimates hearing.

"Our objective in announcing what we've announced today was to take action which allows us to live within our budget for this financial year and to position us for the financial years that lie ahead."

The mining tax, known as the Minerals Resource Rent Tax, imposed a 30 per cent super profits tax on major iron ore and coal mine projects. Laws to abolish the tax passed through the House of Representatives on Wednesday, but faces a more difficult passage through the Senate.

The opposition and Greens have the numbers in the upper house to block the laws, which may force the government to wait until the new Senate sits from July 1, 2014.

Mr Leeper said that while the abolition of the MRRT accounted for about 200 jobs, the remainder of the cuts were due to budget efficiency restrictions imposed by the former Labor government.

Earlier this week, the government said it would review its plan to cut 12,000 public service jobs through natural attrition, due to job cuts already in train through the former government's efficiency dividends, where departments and agencies receive across the board funding cuts.