Terry Moran, who led the Department of Prime Minister and Cabinet under Kevin Rudd and Julia Gillard, said there was "a logic" to most of the department mergers announced by Mr Morrison on December 5.

But Mr Moran said the restructure could quickly become a very costly and disruptive exercise if the government tried to make significant organisational changes.

"If you just take the groups out of a large department and shift them into another department and allow them to continue in what they are doing, the only thing that you are left with to sort out is how to divide up the corporate overheads," the former APS boss said.

"What often causes difficulties with [such] changes is when the shift of a significant area from one department to another is seen as providing an opportunity for a wholesale reorganisation of the new department.

"That is a big mistake. That is what causes disruption, waste of money and poor performance."

Mr Morrison, who is also Minister for the Public Service, has ordered a restructure of the public service to cut the number of departments from 18 to 14 and create four mega-ministries by combining Education with Employment and Skills, Agriculture, Water and the Environment, Industry, Science, Energy and Resources and Infrastructure, Transport, Regional Development and Communications. Services Australia will become an agency within the Department of Social Services.

Work has already begun on implementing the changes, which are due to come into effect by February 1 next year.

The departments involved have begun discussions and several, including Communications, Infrastructure, Education and Employment, have formed interdepartmental committees to support planning and consultation.

Mr Morrison said the mergers were being undertaken to improve the delivery of government services.

But he has given mixed signals on how far-reaching he expects the changes to be.

At the media conference held to announce the restructure, the Prime Minister at one point said that "those who were previously performing functions in...other departments will now perform those functions in new departments", suggesting there might be minimal disruption.

But at the same event he indicated more substantial changes were envisaged.

"The new structures will drive greater collaboration. It [sic] will break down the silos. It'll ensure that important policy challenges in which different parts of the public service are working on, can work more effectively on together. It means better integration in key areas like education and skills and the delivery of regional services."

The restructure is being complicated by government pressure on public service staffing and spending and broader changes to be undertaken as part of the government's response to the Thodey review.

Mr Morrison said he expected department secretaries to manage the changes within their existing budgets and staffing caps, and washed his hands of any job cuts or redundancies that might arise.

"This isn't about any cost savings measures," the Prime Minister said. "I expect...all departments secretaries to be realising maximum efficiencies for how they run their departments every single day of the year. That's their job.

"And whatever decisions they take over the next 12 months, two years, five years, they'll take those decisions. They're not decisions that the Government takes."

It is expected that the reorganisation will result in job losses in public service support roles as back office functions are consolidated, but Mr Moran said any change should be gradual.

He said trying to achieve savings by consolidating support functions, especially IT, was "very hard to pull off".

"If you try to do it on a broad sweeping basis the prospects would be for failure," Mr Moran said.

"If you try to systematically make incremental enhancements to the IT systems you have got a better chance of success."