The new government's aggressive moves on the public service have caused widespread anxiety for workers preparing to clear out their desks and move to other new workplaces.

Differences in conditions and wages in different departments and agencies can run into tens of thousands of dollars in some instances, and many workers have been facing uncertain futures since the shake-up of the bureaucracy was announced five days ago.

But new public service minister Eric Abetz has guaranteed that workers moving departments will continue to have the same conditions while the service chiefs work through the implications of "machinery of government" changes made last week.

The pledges apply to thousands of rank-and-file bureaucrats and to hundreds of high earners in the Senior Executive Service.

In one of its first acts after being sworn in, the new Abbott government announced that AusAID and its 1500 staff, many Canberra based, would 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 Department of Education, Employment and Workplace Relations with its 4400 workers will be split into two separate, stand alone departments, and other changes include Health and Ageing losing its ageing function to the expanded Department of Social Services.

Three department heads were sacked as part of the shake-up, another one agreed to step down in several months, and AusAID's director general went on "extended leave" just hours before his agency's demise was announced.

But the Public Service Commission, the bureaucracy's workplace authority, has announced that all workers displaced by the change will keep their wages and conditions, at least in the short term.

"In the case of an agency that has been abolished, this will mean that terms and conditions of its former employees will continue to be preserved, even though the agency itself has been abolished," the commission said.

"This will give agencies time to work through the implications of receiving employees covered by agreements with potentially significantly different terms and conditions to those of the gaining agency."

But the commission warned that departments would have to work on getting new employees into their enterprise bargaining deals sooner or later.

"As these implications are worked through in the coming weeks, arrangements will be made to release employees from the operation of the determination," the commission said.

The announcement from the commission also acknowledged public servants in the same workplace would be on different terms and conditions and called for collaboration between different parts of the service to make the changes as smooth as possible.

"There will be a period during which some employees working in a single agency or department, particularly new agencies combining functions of a number of former agencies, may have different terms and conditions of employment in comparison to other employees," the commission's circular stated.

"Affected agencies may need to manage multiple sets of terms and conditions of employment for a transitional period.

"It may be most efficient for losing agencies to continue to support transferred employees for a time. Gaining and losing agencies are encouraged to collaborate to minimise transaction costs to the maximum extent possible."