Football Australia has promised strong action against "anti-social behaviour" from supporters at the Australia Cup final after reports of fans making Nazi salutes and shouting over an Indigenous welcoming ceremony.

Australian media reported fans chanted and booed during the Welcome To Country ceremony at Western Sydney Stadium on Saturday, where over 16,000 attended as Macarthur FC recorded a 2-0 win over semi-professional side Sydney United 58

Pictures on social media appeared to show Nazi salutes being made by supporters of Sydney United 58 and the display of symbols associated with the Ustase, a Croatian fascist organisation that ran that country as a puppet state during World War 2.

Sydney United 58 were founded as Sydney Croatia in 1958 and were a powerhouse in the National Soccer League that preceded the formation of the A-League in 2004.

Football Australia condemned the actions of a "small minority of individuals" and said it had evicted eight people from the stadium.

"Football Australia is today assessing all footage and images available of certain individuals which are of concern to our organisation and the broader Australian football community, including the displaying of the 'Hitler salute'," the governing body said in a statement.

"Football Australia is working closely with the management of CommBank Stadium and New South Wales Police to determine strong and swift action on any identified anti-social behaviour, which may also be deemed as illegal in the state of NSW."

NSW Jewish Board of Deputies CEO Darren Bark called for fans who made Nazi salutes to be given lifetime bans.

"These vile symbols and salutes have no place in modern Australian society. They represent the ultimate manifestation of evil," he said.

Sydney United said they were working closely with the authorities to conduct a full investigation.

"Sydney United 58 FC has zero tolerance towards any form of disrespect, racism or discrimination," the club said. "Those that do not align themselves with these values are not welcome at Sydney United 58 FC and their views will never be tolerated."

Former Australia defender Jade North, the first indigenous player to captain the Socceroos, said the behaviour was disrespectful.

"It is extremely disappointing that respect for the cultures and practices of Aboriginal and Torres Strait Islander Peoples is not met by some sections of Australian society today in the same spirit in which it is extended," said North, co-chair of Football Australia National Indigenous Advisory Group.

Professional Footballers Australia co-CEOs Beau Busch and Kathryn Gill said "universal values of fairness, respect and courage" had been "shattered".

"Our sport must now respond and the players are committed to playing an important role," Busch and Gill said in a statement. "An effective response will not be developed by focusing on whether or not these actions were inflicted by a minority."