The fallout was still being felt on Monday after Indigenous speakers at Sydney, Melbourne and Perth services were booed and heckled, sparking condemnation.
Queensland Premier David Crisafulli also raised eyebrows by attending an Anzac Day service on Saturday that did not feature an acknowledgement.
Leading Indigenous activist and academic Marcia Langton on Monday accused the "forces of the right" of perverting Welcome to Country's meaning, calling for more police at dawn services.
Five people reportedly linked to the anti-immigration March for Australia group were ejected from Perth's ceremony.
March for Australia has been behind a series of anti-immigration rallies nationwide, some of which have also featured neo-Nazi speakers and attendees.
"I think there should be a greater police presence to protect those who observe Anzac Day," Professor Langton told ABC Melbourne on Monday.
There were 15 move-on orders issued across WA, while several people were ejected from the 11,000-strong Sydney crowd, with one charged with committing nuisance.
Prof Langton said the problem was people who heckled Welcome to Country did not know anything about it.
"They think it is Welcome to Australia, it's not. It's welcome to the Country of the original people where the Anzac ceremony is being held," she said.
"The forces of the right have perverted the meaning of the Welcome to Country ceremony and turned it into a very ugly nonsense."
Opposition Leader Angus Taylor condemned the booing but suggested Welcome to Country ceremonies might be overused.
Asked for her response, Prof Langton said: "When I was at school every morning we had to stand on parade and sing the national anthem - that was overdone.
"A Welcome to Country or Acknowledgement of Country is usually very brief ... it's infrequent, only for special occasions.
"It's a very polite and gracious way to acknowledge the Traditional Owners."
Deputy Prime Minister Richard Marles took aim at Mr Taylor's claim, saying the "overwhelming response" from Australians to the Anzac Day booing was outrage.
Mr Marles stressed Anzac Day was also about acknowledging the long history of Indigenous Australians' service in the defence force.
This year marks the 75th anniversary of the Battle of Kapyong, where Captain Reg Saunders, Australia's first Indigenous army officer, served with distinction.
"All of that should be acknowledged and celebrated on Anzac Day, and this booing has no place," Mr Marles said.
Meanwhile, the Queensland premier has come under fire for attending a Townsville dawn service that did not include a Welcome to or Acknowledgement of Country.
State minister John-Paul Langbroek on Monday said he had also attended a Gold Coast function that did not include the ceremonies.
He said RSL branches were responsible for co-ordinating their Anzac Day service protocols, not the state government.
"The important issue is that the publicity about the one the premier attended in Townsville was that it was not arranged by the state government," Mr Langbroek told reporters on Monday.
RSL Queensland has been contacted for comment.
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