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The world number one tennis player was denied entry to Australia due to an issue with his visa.
Authorities noticed a mistake with the player's application when he arrived in Australia.
The Australian Open was due to be played by the Serbian player.
His lawyers will challenge the decision to deport him, Australian media report.
The tennis star was questioned at the airport for hours while his visa and exemption status was being investigated.
His team did not request a visa that would allow for medical exemptions. It is not clear if he will stay in Australia while his lawyers try to overturn the decision.
Last year, he said he was opposed to vaccinations.
The Australian Border Force said in a statement that the visa of the man had been canceled because he failed to provide appropriate evidence to meet the entry requirements.
"Non-citizens who do not hold a valid visa on entry or who have had their visa canceled will be removed from Australia," it said.
His treatment has caused outrage in Serbia. Srdjan said his son was in a room guarded by police.
He said in a statement that the fight was not just for Novak, but for the whole world.
The whole of Serbia supported the star, who was a victim of "harassment", according to the president.
Australia's Prime Minister Scott Morrison said that he would refuse entry to the country if he didn't have proof that he could not be vaccine free.
Australia is seeing tens of thousands of Covid-19 cases for the first time after enduring some of the world's strictest restrictions. Some people can't travel interstate or globally because of current measures, but more than 90 percent of Australia's over-16 population is fully vaccine free.
The Australian Open will be held in January.
