Prime Minister Tony Abbott has refused to explain why he sacked three top bureaucrats, saying that he respects the "integrity" of the public service.

Yesterday, Mr Abbott announced that the secretaries of three departments had had their contracts terminated and that Treasury Secretary Martin Parkinson would step down next year.

The Labor Party has roundly criticised the sackings as "ruthless" and motivated by a political agenda.

But the Prime Minister has emphasised how much he respects the public service.

"I'm not going to get into the whys and wherefores of individual decisions," he said.

"Obviously there were a couple of departments that were merged but I think you can see from what we've done that we respect the professionalism of the public service.

"We respect the integrity of senior members of the public service."

Under new ministerial arrangements, two of the departments involved - Resources, Energy and Tourism and Innovation, Industry Science and Research - have had their responsibilities rolled into other portfolios.

AusAID rolled into Foreign Affairs Department

Another major change - to bring Australia's aid agency, AusAID, into the Foreign Affairs Department - has also been criticised as a backwards step.

Mr Abbott says it will mean Australia's aid program is "fully integrated into our overall diplomatic effort".

It is not clear whether that will mean any jobs will be lost, but he has confirmed the agency could lose staff as part of the Government's overall aim to cut public service numbers.

"We do intend to trim the size of the Commonwealth public sector by 12,000 through natural attrition over the next three years," he said.

"So, yes, there may well be fewer people working in AusAID in three years time than is now the case."

The ABC understands the Director General of AusAID, Peter Baxter, has resigned, although the Government says he has taken extended leave.

Mr Abbott is also fending off continuing criticism of the lack of women in his ministry.

Out of 42 positions, just six are held by women and only one is in the ministry - Foreign Affairs Minister Julie Bishop.

Liberal backbencher Wyatt Roy has criticised the gender imbalance as "not good enough".

Mr Abbott has also brought back the Office of Women under his department, and appointed WA Senator Michaelia Cash as Minister Assisting the Prime Minister for Women.

He says the Government will deliver "good policies" for all Australians "including women".

"The best thing that can be done for women in the near future is put in place a fair-dinkum paid parental leave scheme, that's what will happen under the incoming Coalition Government," he said.