About 50 people came together at the shopping centre for the rally and began singing the song, which seems to have become a common theme across rallies in Melbourne.
The group sung together for five minutes before scattering when police arrived.
Now, the singer's manager Glenn Wheatley is making sure to distance John from the protests.
Speaking with The Age, Glenn said, "It's something that John and I do not condone, the use of that song, particularly in a time in Melbourne where we are in Stage Four lockdown"
"Really, the last thing we should be doing is protesting, no one should be hitting the streets en masse, endangering people’s lives and livelihoods."
He added the song has previously been used in far-right demonstrations within Australia, which was "not what we want to see the song used for"
"It was not meant to be a protest song, it was meant to be used as an inspirational song for nations and for people, not in a situation of what was an illegal protest.
He added that while he and John support people's right to protest, now is not to the time to be gathering in large crowds in Melbourne.
Two people were arrested and six people were fined for their participation.
Protestors were being directed to continue the closed Footscray Market on the other side of the city after leaving Chadstone, however, police were already at the market so it didn't go ahead.
A spokesperson for Victoria Police said, "We are frustrated that these people continue to put the lives of Victorians at risk."
"While we know the majority of the community are doing the right thing, the behaviour of these selfish few who choose to blatantly ignore the directions will not be tolerated.
"We will continue to take the same swift and firm action against those who choose to blatantly ignore the directions, and our investigations will continue."