Tony Abbott has announced the sacking of three public service chiefs and a major shake-up of the federal bureaucracy in the first few hours after he was sworn in as Prime Minister.

Mr Abbott and his 41 ministers, assistant ministers and parliamentary secretaries were officially commissioned by Governor-General Quentin Bryce at Government House in Canberra on Wednesday morning.

The ceremony had barely finished when the Prime Minister's office issued a press release, announcing three departmental secretaries had had their contracts terminated and the Treasury Secretary would stand down next year.

"Each of these secretaries has made a substantial contribution to public life in Australia and I wish them well for the future," Mr Abbott said in the statement.

Dr Don Russell lost his job as head of the Department of Innovation, Industry, Science and Research; Blair Comley was the head of the Resources, Energy and Tourism Department; and Andrew Metcalfe, a former Immigration Department chief, has been sacked as head of the Agriculture Department.

The ABC has obtained an internal departmental email from Mr Metcalfe, who has worked just under 34 years in the public service.

"While I am naturally disappointed that I will no longer be working with you, I of course accept and respect the Government's decision," he said.

The Treasury Secretary, Dr Martin Parkinson, has also told new Treasurer Joe Hockey he will stand down in the middle of 2014.

The statement says the Abbott Government will discuss a "further appointment" with him next year.

Former deputy prime minister and Labor leadership aspirant, Anthony Albanese, says there is a political agenda behind the dismissals.

"These jobs should not be political playthings. These jobs are important," he said.

"We have professional public servants - they should be respected."

Former Treasurer and now Labor backbencher Wayne Swan has praised Dr Parkinson for this work.

Treasury Secretary Martin Parkinson is a talented public servant who will be a loss to Treasury when he steps down next year — Wayne Swan (@SwannyQLD) September 18, 2013

Changes made to departmental structure

Mr Abbott has also announced significant changes to the public service following a reorganisation of several portfolios.

AusAID, Australia's overseas aid agency, will be integrated into the Department of Foreign Affairs and Trade (DFAT), to make diplomacy and aid delivery "more closely aligned".

The ABC understands AusAID's director-general Peter Baxter has resigned, but the Government disputes this.

A spokesperson for Foreign Affairs Minister Julie Bishop says Mr Baxter has taken extended leave and the Government looks forward to his continued service in another senior official role.

DFAT will also take on responsibility for the overseas promotion of Australia as a tourist destination.

Archie Law, executive director of charity ActionAid Australia, says the AusAID move will see the aid budget used to promote Australia's national interests.

"The Government's short-sighted decision to integrate AusAID into DFAT will have massive and devastating effects on Australia's aid program and on the people living in poverty that the program supports," he said in a statement.

"AusAID has been delivering an aid program that eradicates poverty in the world's poorest communities, while DFAT's objective is to promote and protect Australia's national economic and political interests.

"We want to see this Government stand by its foreign policy and deliver an effective aid program."

As flagged earlier, the Customs and Border Protection Service will move from the Attorney-General's portfolio to new Immigration Minister Scott Morrison.

The Immigration Department will lose responsibility for settlement services for refugees and migrants; that will move to Social Services, under Kevin Andrews.

Mr Andrews will also take on responsibility for aged care and programs for people with a disability.

It is unclear what impact the changes will have on public service staff levels.

The Coalition has promised to cut 12,000 Commonwealth public service jobs over the next four years, through natural attrition, with the aim of saving $5 billion from the federal budget.

Tony Abbott's day of 'action' on carbon tax, TPVs

The Prime Minister described his first official day in office as "an action day" and declared he would "immediately" begin work to repeal the carbon pricing scheme, and bring back the Howard-government style temporary protection visas (TPVs) for asylum seekers who arrive by boat.

At the swearing in ceremony, Mr Abbott promised his Government would "strive to govern for all Australians, including those who didn't vote for us".

"We won't forget those who are often marginalised; people with disabilities, Indigenous people and women struggling to combine career and family.

"We will do our best not to leave anyone behind.

"We hope to be judged by what we have done rather than by what we have said we will do.

"And we will not spare ourselves... in order to deserve the trust placed in us this day."

Many of the new ministers arrived at Government House with their families, including some very young children.

The new Agriculture Minister, Barnaby Joyce, arrived in a taxi with his family, after he quit the Senate to reclaim the Lower House seat of New England for the Nationals.

The Prime Minister's chief of staff, Peta Credlin, and her husband Brian Loughnane, who is the Liberal Party's federal director, also attended the ceremony.

After the ceremony, Mr Abbott presided over his first ministerial meeting where he told his frontbench "the responsibilities start now".