They tweeted: "The fire brigade were quickly on the scene and the AOC's emergency plan was put in place."
The fire involved two pieces of cardboard in a basement car park, Rio 2016 officials said.
The Australian delegation initially refused to move into the building on Sunday citing "blocked toilets, leaking pipes and exposed wiring".
"The incident in the basement car park of building 23 in the Olympic Village was quickly controlled by the fire authorities who are constantly present," said Rio 2016 media manager Philip Wilkinson.
"The occupants of the building were evacuated and were allowed to return inside the building after 30 minutes. The incident is being investigated."
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The Australian Olympic Team have confirmed there was a "small fire" in the basement of their building in Rio.