Martin Parkinson says former prime minister Tony Abbott damaged the bureaucracy when he sacked him.

Dr Parkinson, chief of the Department of the Prime Minister and Cabinet says he holds “no personal animus” towards Mr Abbott over a series of public service leader sackings in 2013, including his own dismissal as Treasury secretary.

Dr Parkinson told Melbourne University's Policy Shop podcast that the sackings came as a result of following legally mandated directions from former Labor government.

“When Tony Abbott then decided to dispense with us, I didn't take that personally," he said.

“During that period, 15 months when we knew I was going, we had a perfectly professional relationship. Very open and honest, he asked me my views, I told him.

“He listened respectively. Sometimes he agreed, sometimes he didn't and you couldn't ask for anything more.”

But Dr Parkinson says it was still damaging to the APS, “because there were instances after that happened of senior colleagues reporting their staff saying; ‘Well, I'm not going to put my hand up for a controversial role because this is what happens.

“You follow on the democratically elected, legally mandated directions of the government of the day and you get sacked as a result.”

Dr Parkinson was later brought in by Malcolm Turnbull to lead PM&C after Mr Abbott was rolled in 2015.

He said returning to the public service was difficult.

“Now I think a lot of water's gone under the bridge since then and those sorts of concerns in the public service have been ameliorated, but there's no question that for the service as a whole, I think it came as quite a shock,” Dr Parkinson said on the podcast.

“I'd never sort of looked at secretary of Prime Minister and Cabinet and thought, that's a job I want to do.

“I'm the first person who's ever both been secretary of the Treasury and then secretary of Prime Minister and Cabinet ... the idea of coming back to do it caught me by surprise when the Prime Minister asked me to do it.

“But Prime Minister Turnbull can be very, very persuasive and as somebody who is a public servant in the true sense of that word of serving the people of Australia through the government of the day.

“If the prime minister of the day asks you to do something, you better have a very, very good reason to say no. When I thought about the reasons I, on balance, felt that it was a bit hard to say no to a prime minister.”

Dr Parkinson also said public servants should not have to advocate for partisan decisions.

“I think the public service has to constantly come back to the fact that it serves the people of Australia through the government of the day, but the fact is the people of Australia can change the government,” he said.

“At all times, you have to act with professionalism and integrity and it's fine to explain government policies, but public servants can never become advocates for a particular policy because advocacy means you've moved from that sense of impartiality to taking one side or the other.

“I think it's less well understood by some of the more recent members of either side of politics, and it's less well understood, I think, by the cross benches.”