Mr Morrison said he would not precondition any requirement of allowing Djokovic to return earlier, amid the intense international spotlight on the turbulent saga.
“There is the opportunity for [an individual] to return and in the right circumstances, and that would be considered at the time,” Mr Morrison told 2GB Radio.
Djokovic had previously been freed from immigration detention after a Federal Circuit Court judge ruled an initial decision to cancel his visa last week be overturned.
The result then forced Immigration Minister Alex Hawke to exercise his ministerial powers to intervene in the case to deport the Serbian national on Friday evening.
Djokovic has addressed the outcome, saying he was “extremely disappointed” and would cooperate with the decision.
Mr Morrison has defended his government’s handling of the case, saying it never gave him a medical exemption.
“The federal government gave him no such exemption,” he said.
“If you come in from overseas, and you have a visa, wherever that visa is, you either have to be vaccinated, or you have to have a valid medical exemption and those things weren’t achieved.”
PM denies double standard on anti-vaccination
During the latest court appeal, Mr Hawke had claimed the presence of a “high-profile” athlete like Djokovic, who is unvaccinated, could foster “anti-vaccine” sentiment and “civil unrest” in Australia.
But the prime minister has denied a double standard being applied to his government politicians who have voiced concern over vaccine requirements within his own ranks.
“I think you’re conflating two different issues being in Australia – you’re an Australian you’re a citizen, you’re a resident and you can be here and express your views,” he said.
“If you’re someone coming from overseas, and there are conditions for you to enter this country. Well you have to comply with them it’s a simple as that.”
Djokovic departs Australia after court upholds visa cancellation
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Coalition members such as George Christensen, Alex Antic and Gerard Rennick have repeatedly voiced opposition to so-called vaccine mandates to work and attend certain venues.
This included Mr Christensen using a speech in Parliament last year to call for civil disobedience to oppose the measures.
Labor’s Home Affairs spokesperson Kristina Keneally said the government’s failure to reign in these members stood in contrast to its stance on Djokovic.
“Mr Morrison cannot pretend he is a wolf – tough on Novak Djokovic but a lamb in front of his own party room unwilling to tell people like George Christensen to pull their head in,” she told the ABC.
She welcomed the decision to deport Djokovic, but stressed the government had “bungled” the situation.
“This has been a monumental bungle at our borders by the Morrison government,” she said.
“They want to run around and pat themselves on the back about it. They deserve a kick up the backside.”
Home Affairs Minister Karen Andrews said despite international attention on the deportation, Australia has not been publicly embarrassed by the decision.
“I understand that this has played out very publicly,” she told the ABC.
“[But] Australians can be very confident that the Morrison government and its ministers will do all that they can to ensure we have strong borders.”