The man, in his 20s, was taken to Gold Coast University Hospital in Queensland state by paramedics wearing full protective gear.
He returned from west Africa two days ago and has been seriously ill since.
Gold Coast health officials said he was displaying Ebola symptoms, including fever, but an initial assessment suggested it is unlikely he has the killer disease.
"We are managing him in accordance with the standard national protocols for isolation of patients who are potentially at risk of Ebola disease," the director of infectious diseases at Gold Coast University Hospital, John Gerrard said.
Test results are expected later today.
Health officials added that the hospital had the necessary processes in place "to safely manage such circumstances".
More than 2,200 people have died in the Ebola outbreak gripping west Africa, with more than 4,200 cases in Liberia, Sierra Leone, Guinea and Nigeria leaving medical teams in those countries overwhelmed.
The World Health Organization has predicted an "exponential increase" in infections across west Africa, and warned that Liberia alone will face thousands of new cases in the coming weeks.
Sanjaya Senanayake, an infectious diseases physician at the Australian National University Medical School, described the case as a wake up call.
"Even if this isn't Ebola virus infection, this case will give the health service an opportunity to see if the protocols can be successfully implemented or have steps that still need to be ironed out.
"Feedback of the outcome of this by the Gold Coast hospital to other health jurisdictions is important so everyone can tighten their protocols in the event of another case appearing on our shores.
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