Outgoing Health Department secretary Glenys Beauchamp will stay on, while her replacement deals with the coronavirus pandemic.
Ms Beauchamp went on leave last Friday, ahead of her retirement on February 28, ending a 21-year career in the Australian Public Service.
She will be replaced by Chief Medical Officer Brendan Murphy.
But Health Minister Greg Hunt said Ms Beauchamp offered to return to work over the weekend while the incoming department secretary handled the outbreak of the virus.
"The secretary Glenys Beauchamp pre-empted us before anyone else got to the question of it on Australia Day, when we spoke," Mr Hunt said.
"[She said] 'I think I should be back on deck'.
"She's been tremendous."
Professor Murphy said he would continue as chief medical officer until further notice.
"I'm focusing entirely on [the coronavirus] issue at the moment," Mr Murphy said.
"We will assess the situation on a regular basis and I'll consult with the minister about what the appropriate time is."
Meanwhile members of the Australian Public Service have been told they should either work from home or be given miscellaneous leave if they have been potentially exposed to coronavirus through recent travel or contact with an infected person.
However the Community and Public Sector Union called for that to be extended to labor hire staff as well.
"The department must ensure this staff cohort are not financially impacted and will be given access to the same leave," CPSU secretary Melissa Donnelly said.
However the Australian Public Service Commission said leave arrangements could not be extended to contractors, as they were not covered under the same enterprise agreements as full-time staff.
Individual agencies could make agreements with contractors on a case-by-case basis, the commission said.
The World Health Organisation has now declared the virus a public health emergency.
There are nearly 8000 cases of coronavirus worldwide, including nine in Australia across three states.
The death toll remains at 170, although Professor Murphy warned that could change.
The number of infections have surpassed the SARS outbreak of the early 2000s.
The Australian government is warning people to reconsider their travel to China and to avoid the Hubei province where the outbreak began altogether. The United States is advising against all travel to China.
Foreign Minister Marise Payne is locked in negotiations with Chinese authorities to allow around Australian citizens trapped in Wuhan to be evacuated. The evacuees would have to spent 14 days in quarantine on Christmas Island before being allowed to return to the mainland.
Mr Hunt said the first medical team had arrived on the island and would finish setting up a "deployable" hospital by the end of the weekend. The hospital would include a negative pressure room, isolation and critical care facilities.
Professor Murphy said despite the World Health Organisation declaration, containment of the outbreak "is the goal and still possible".
The Transport Workers Union has called on Australia to cut flights to China, amid concerns over the health risk to aviation workers and the general public. Qantas is still operating daily flights to China.
Professor Murphy said the World Health Organisation had strongly recommended that nations do not ban flights to China. He said the airlines that had cut flights so far had done so for commercial reasons.
"Unless you lock down exit from the country, banning flights, direct flights, doesn't stop people coming from China. They could come from all sorts of other ports and at least [with flights] we know who is coming from China and we can meet and do very intensive border measures," Professor Murphy said.
What we know about coronavirus
- There are 98 confirmed cases of infection outside mainland China in at least 18 countries including Thailand, Japan, Hong Kong, Singapore, Taiwan, Australia, the United States and France.
- No deaths have been reported outside China.
- The World Health Organisation declared the outbreak a public health emergency of international concern on Thursday.
- The United States reported its first case of person-to-person transmission. Germany, Vietnam and Japan have also recorded similar transmissions, which suggest greater potential for the virus to spread further.
- Several Chinese cities have introduced strict travel curbs.
- Global airlines have suspended or scaled back direct flights to China's major cities.
- Countries including Australia, Canada, France, Germany, Indonesia, Italy, Japan, Singapore, South Korea and the United States are working to evacuate citizens from Wuhan or have already started.
- Nearly 200 evacuated Americans arrived at a US military base in California to be isolated for at least 72 hours.
- Three Japanese evacuated on a government-chartered flight proved to be infected, including two who had not shown symptoms.
- The Chinese Football Association said it would postpone domestic games in 2020.
- The World Athletics Indoor Championships scheduled in the Chinese city of Nanjing in March have been postponed until 2021.
- Alphabet Inc's Google and Sweden's IKEA said they were temporarily shutting all offices and stores in China over the outbreak.
- with Sally Whyte