Prime Minister Tony Abbott's first day in the job has seen three top Canberra public servants sacked, another one resign, two departments axed and a major high-profile agency abolished.

Mr Abbott moved aggressively on the public service on Wednesday, sacking the secretaries of the Agriculture, Industry and Energy departments.

The head of AusAID, Peter Baxter, went on ''extended leave'' just hours before the abolition of his agency was made public and Treasury chief Martin Parkinson has agreed to step down in mid-2014.

AusAID and its 1500 staff, many of them Canberra-based, will be absorbed into Foreign Affairs and Trade.

The Department of Regional Australia, Local Government, Arts and Sport, which has about 700 workers, will be abolished and its duties broken up as will the Department of Resources, Energy and Tourism and its 590 employees.

The highest profile sacking is that of Andrew Metcalfe from the Agriculture Department.

Mr Metcalfe led the Immigration Department from 2005 to 2012 in a tenure that spanned Liberal and Labor governments and, as a former Liberal staffer, was thought to enjoy good relations with both sides of politics.

But the veteran public servant, who is less than a year away from being able to access his Commonwealth superannuation benefits, may have made enemies in the Coalition from his close association with the Labor government's failed "Malaysia solution'' to asylum seeker boat arrivals.

He also publicly disparaged the idea of turning back asylum seeker boats, a move that is now at the heart of Coalition policy.

Once seen as a potential head of the Department of the Prime Minister and Cabinet, Mr Metcalfe has been in charge at Agriculture since January 2012.

The other two casualties are Don Russell at the Industry Department and Blair Comley at Resources, Energy and Tourism.

Dr Russell, a former ambassador to the US with a long association with Labor, had been tipped to quit the public service rather than serve a Coalition government.

Mr Comley had been at Energy and Resources, which is also to be scrapped, for six months before he was sacked on Wednesday and was the last secretary of the now-defunct Climate Change Department.

Both Mr Comley and his mentor, Dr Parkinson, who also served as head of the Climate Change Department, were closely associated with the design of the carbon price, the piece of Labor policy most hated by the Coalition.

Dr Parkinson was forced before this month's election to mount a robust defence of his department's performance in the face of Coalition attacks and accusation that Treasury had been "politicised".

The government says it will consult with Dr Parkinson about a new role when he steps down from Treasury in mid-2014.

Wednesday's shake-up saw the appointment of two new departmental secretaries with former ACT Justice and Community Safety chief Renee Leon taking over a new, stand-alone, Employment Department.

Lisa Paul has been appointed as the Secretary of the new Department of Education, which will also be split from Employment and Workplace Relations.

Paul Grimes will move from Environment to take over from Mr Metcalfe at Agriculture.

Mr Metcalfe, Dr Parkinson, Dr Russell, Mr Comley and Mr Baxter were all contacted for comment on Tuesday, but declined.