Prime Minister Anthony Albanese confirmed the senior public servant had been appointed the top job for the next five years from Saturday.

Mr Cook will replace outgoing secretary Michele Bruniges, who has been in the role since April 2016.

He is currently the department's deputy secretary across higher education, research and international and has previously held a number of other senior roles within the Victorian and Queensland education departments.

"Mr Cook brings to his new appointment significant policy experience and strong stakeholder relationships, particularly in the education sector," Mr Albanese said in a statement on the Friday.

"He was awarded a Public Service Medal in 2014 in recognition of his work on school policy and funding reform."

READ MORE:

Peak tertiary body Universities Australia welcome the news, describing Mr Cook as a "skilled leader with a deep understanding of, and appreciation for, higher education".

"Universities have forged a strong working relationship with Mr Cook during his tenure as a deputy secretary overseeing higher education and research policy," chief executive Catriona Jackson said on Friday.

"We look forward to building on that as we begin the first comprehensive review of the higher education sector in more than a decade, and beyond."

Mr Albanese also thanked Dr Bruniges, whose last day is on Friday, for her nearly seven years in the role.

"Dr Bruniges has made a significant contribution to education policy at the Commonwealth and state levels over a number of decades and I wish her well for the future," he said.

Dr Bruniges marks the second long-serving secretary to end her time in the top job this year after the departure of former Veterans' Affairs secretary Liz Cosson last month.

The terms for Home Affairs secretary Michael Pezzullo and Treasury secretary Dr Steven Kennedy will end next year.

We've made it a whole lot easier for you to have your say. Our new comment platform requires only one log-in to access articles and to join the discussion on The Canberra Times website. Find out how to register so you can enjoy civil, friendly and engaging discussions. See our moderation policy here.