Professor Baggoley, who is set to retire on Friday, will be replaced by Professor Brendan Murphy, who has been chief executive of Victoria's Austin Health since 2005.

Health department secretary Martin Bowles said Professor Baggoley had been an "influential figure in the nation's response to numerous challenges and threats to our health".

"In particular, he has been outstanding in progressing the nation's response to antimicrobial resistance, vaccine preventable disease, the risk of new communicable diseases, and improved screening and early diagnosis of non-communicable diseases such as cancer," Mr Bowles said in a statement.

Professor Baggoley led Australia's response to the Ebola outbreak in West Africa and the recent Zika virus.

He also supervised the country's monitoring of the Middle East Respiratory Syndrome Coronavirus (MERS) and led the international effort to minimise the threat from the disease through his involvement with the World Health Organisation, Mr Bowles said.

Mr Bowles said Professor Murphy would take up the top job from October.

"Professor Murphy is an experienced clinician but also highly experienced in stakeholder management, strategic direction-setting and policy advice," he said.

Professor Murphy is a director of the Florey Institute of Neuroscience and Mental Health, the Olivia Newton-John Cancer Research Institute and the Victorian Comprehensive Cancer Centre and Independent Chair of Health Services Innovation Tasmania.

Dr Tony Hobbs has been appointed deputy CMO and will be the acting CMO until October.