Unvaccinated Australian Open champion Djokovic had his visa revoked by the Australian government on Friday, throwing doubts over his ability to defend his title.
Unless he wins an appeal, he will be deported from Australia.
Murray described the situation as 'not good for anyone', telling reporters in Sydney that he didn't want to 'kick' Djokovic when he was down.
"Look, my feeling is that I would encourage people to get vaccinated, but yeah, I do feel like people should be able to make their own decision," said the Briton, shortly after making the final of a warm up tournament in Sydney.
"Ultimately people have to make their own choices. But there is also consequences, sometimes, for those decisions, as well."
Djokovic's legal team submitted their request for an injunction late at night, less than three hours after Australian Immigration Minister Alex Hawke used discretionary powers to revoke the visa.
The controversy has intensified a global debate over the rights of the unvaccinated.