Songwriter John Schumann has been shocked to learn the anthem he wrote, I was only 19, was performed at at least one Reclaim Australia rally.
The group's supporters held rallies around the country on Saturday to oppose "sharia law, halal tax and Islamisation".
Violence erupted when they clashed with anti-racism groups.
Schumann said the song, I was only 19, was written to help people understand the plight of Vietnam veterans.
Like his other songs, it was about compassion, tolerance and inclusiveness, he said.
"I am very, very disappointed to see my work co-opted by what I, at my most charitable, consider to be a very confused `patriotic' movement," Schumann said in a statement on Sunday.
The song honours all Australians who have put themselves in harm's way for their country, he said.
"It is not to be used to advance ignorance and intolerance, especially as we approach the centenary of Anzac," he said.
A Youtube video shows the song being performed at Reclaim Australia's Gold Coast rally.
There were several arrests at the rallies, including three in Melbourne where more than 3000 people clashed in Federation Square and blocked surrounding streets.
Hundreds of police formed barricades to separate protesters but scuffles still broke out and some people were treated by paramedics for minor injuries.
Earlier on Sunday, federal Opposition Leader Bill Shorten said there was no excuse for the violence.
"There's no place for violence in any protests or any expressions of freedom of speech," Mr Shorten told the Nine Network.
He also said any suggestion that Muslims were planning to bring Sharia law to Australia was exaggerated.
"It was 50-60 years ago people said that the Irish Catholics or the Catholics were trying to take over the joint - and that wasn't true either," he said.
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