Ms Beauchamp, whose abrupt departure has caught many by surprise, is the fourth senior woman appointed by former prime minister Malcolm Turnbull to head a government department in September 2017 who has lost or left her position under Scott Morrison. She joins Kerri Hartland, Renee Leon and Heather Smith, who lost their jobs in the restructure of the public service in December last year.

Her departure means that in less than two months the representation of women at the top level of the Australian Public Service has shrunk from nine out of 18 department secretaries to six out of 14.

The government has selected the nation's chief medical officer, Professor Brendan Murphy, to replace Ms Beauchamp.

Professor Murphy, who is currently spearheading the national response to the coronavirus outbreak centred in China, has served as the principal medical adviser to Health Minster Greg Hunt since 2016 and heads the Office of Health Protection.

He will become the first medical doctor appointed as secretary of the Health Department. When Dr Gwyn Howells led the department from 1973 to 1982 his title was director-general.

Before becoming Chief Medical Officer, Professor Murphy was chief executive officer at Austin Health in Victoria.

Australian Medical Association President Dr Tony Bartone hailed Professor Murphy's appointment as an "inspired choice".

"Brendan has been a respected, knowledgeable, and effective Chief Medical Officer, and the AMA has enjoyed a productive and professional working relationship with him in that role," Dr Bartone said.

"He has been an active and informative leader and great communicator, as exemplified by his rapid response to the current Coronavirus emergency coming out of China.

"He will bring a highly-appropriate and unique mix of skills and experience to his new position."

Ms Beauchamp is also a member of the Sports Australia Board that is at the centre of the sports grant furtore that has engulfed the Morrison government.

Ms Beauchamp has been an ex officio member of the Sports Australia Board since 2017, and attended all seven board meetings in 2018-19, which included the period when Community Sport Infrastructure Program grant applications were the subject of board consideration and assessment.

In a damning report on the administration of the program, the Commonwealth Auditor-General Grant Hehir found that the office of then-sports minister Bridget McKenzie ignored and overrode Sport Australia's assessments and came up with its own list of approved projects.

Mr Hehir's report showed that the Sport Australia Board was sidelined in the process to select grant recipients. Of 236 projects worth $29.7 million in the first round of funding, almost half had been selected by the sports minister despite not being recommended by the board. The auditor found the board "did not play a role" in selecting successful applicants in the two subsequent funding rounds, worth around $70 million.

Health Minister Greg Hunt has confirmed that Ms Beauchamp, who has led the Health Department for a little more than two years, will go on leave from Friday ahead of her retirement on February 28, ending a 21-year career in the Australian Public Service.

A spokesman for Prime Minister Scott Morrison said there was no link between Ms Beauchamp's departure and her position on the Sport Australia Board.

He said her retirement had "nothing to do with anything else", and its conjunction with the sports grant uproar was "completely coincidental".

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Mr Hunt said Professor Murphy had 40 years of experience as a doctor, medical researcher and senior executive.

"He has held a range of board positions including at the Florey Institute, Olivia Newton-John Cancer Research Institute and the Victorian Comprehensive Cancer Centre," Mr Hunt said in a statement.

There had been speculation that Ms Beauchamp would be one of the department heads to be dumped in the sweeping changes announced last year, but she was confirmed in her position.

In a statement issued on Wednesday, Mr Morrison paid tribute to Ms Beauchamp's 21-year career in the Australian Public Service, including nine years at secretary level for several departments including Health, Industry and Regional Australia.

In 2010 she received the Public Service Medal for outstanding service in coordinating the Commonwealth's response to the 2009 Black Saturday bushfires in Victoria.

"Ms Beauchamp has served the Australian people with distinction of her 21-year career," the Prime Minister said. "On behalf of all Australians, I thank Ms Beauchamp for her service."

Mr Hunt also paid tribute to Ms Beauchamp.

"Ms Beauchamp has served the Australian people with distinction over her 21 year career in the Australian Public Service, including nine years at secretary level, as well as 13 years in the ACT public service," he said.

"In her time as secretary of Health, she has been instrumental in improving health services for the Australian people, including a focus on mental health, increased medical research, funding life-saving medicines and strengthening our relationships with the health community."

Professor Murphy's deputy, Professor Paul Kelly, will be acting chief medical officer while a formal appointment process is undertaken.