"When it says 'we are young' it completely disregards the Indigenous Australians who were here before us." Aboriginal culture stretches back tens of thousands of years before the British began colonising Australia in the late 1700s.
They remain among the most disadvantaged Australians, with higher rates of poverty, ill-health and imprisonment than any other community.
Harper said she arrived at the decision to protest herself, but had discussed the issue with her parents.
Harper was trying to "raise awareness and get people thinking about institutionalised racism... and how that might feel to people who these kinds of things affect", he added.
"The school has been respectful of the student's wishes and has provided other alternatives including remaining outside the hall or not singing during the national anthem," a spokesperson said in a statement.
The department denied earlier reports that Harper faced suspension or expulsion for her protest.
Harper's stance on the anthem, with echoes of the kneeling protests of NFL players in the United States, irked Australia's most prominent conservative figures.
Australian politician Pauline Hanson, who has made a career of leaping on such controversial issues, labelled Harper "a brat", before taking aim at the parents for encouraging "divisive" behaviour.
"Here we have a kid that has been brainwashed and I tell you what, I would give her a kick up the backside," the 64-year-old said in a video posted to Facebook.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)