The department said the man worked at the Holiday Inn hotel at Melbourne Airport, and it was contacting the hotel along with the case's close contacts.
The worker returned a negative test result on 4 February and returned to work on 7 February, where they developed symptoms and tested positive.
"We are contacting Holiday Inn Airport workers and others who are considered primary close contacts," the department said.
"They are required to immediately isolate, get tested and remain isolated for 14 days."
Warning in NSW
NSW Health has issued a precautionary alert for sites in Wollongong and south-eastern Sydney after a returned overseas traveller tested positive to Covid-19 two days after leaving their mandatory two-week hotel quarantine.
In a statement issued on Sunday evening, the health department said the person was not showing any symptoms, but had been tested on day 16 as part of an enhanced follow-up strategy for people returning from overseas.
They returned two negative tests during their 14 days in isolation.
The statement said the person has a low level of infection and their household contacts have so far returned negative results.
Their close contacts have already been identified and are in self-isolation.
The statement said investigations so far suggested the person was infected overseas, and there was no indication at this stage of transmission in hotel quarantine.