Patrick Carrigan backed players' right to express their beliefs, saying the anthem debate could prompt discussion beyond football.
The issue has drawn criticism during the tournament, with Kotoni Staggs and other Indigenous Kangaroos players, including Latrell Mitchell, declining to sing before matches.
Staggs, who has made nine appearances for Australia since his 2023 debut, said: "I'm a proud Wirajudri boy and I'm proud of who I am and where I come from and me not singing an anthem doesn't mean that I'm not grateful."
He added: "I still love wearing that jersey, when the anthem is getting played you look around and get emotional."
Staggs said his choice reflected respect for his ancestors, elders and family, rather than a lack of pride in Australia.
"I'm a proud Australian as well but at the end of the day it's just something that I've lived by, and I've got no harm in it. It doesn't take anything away from the jersey I wear."
Former Australia Test coach Mal Meninga has also defended players' position.
Carrigan said: "I know that each and every boy here is proud to pull on the green and gold."
The debate comes as Australia prepare to face Samoa in Sunday's World Cup semi-final at Sydney's Allianz Stadium.