"It says "Advance Australia Fair" and when it was originally written it meant advance Australia for white skin people", she told SBS News.
The school's principal had met with Harper and her parents to discuss alternatives to her protest, the Queensland state education department said.
Harper's protest was in light of her belief that the song doesn't do justice to the contributions of the aboriginal peoples of Australia.
While her father, Mark Nielsen, said he and Harper's mum Yvette Miller are "proud" of their "incredibly brave" daughter for standing up for something she believes in.
Quarterback Colin Kaepernick took a knee as the USA national anthem was played to protest racism.
"It's about who we are as a nation, it's part of us ..."
Prominent politicians have attacked Nielsen and have asked the school to kick her out.
Of the punishment, the young girl said, "I felt like they were trying to take my power away and that made me feel a bit upset because everything that I fight for is for equality and for equal power for everyone".
"When it says we are young it completely ignores the fact that indigenous culture was here for over 50,000 years before colonisation".
Using her astonishingly verbose vocabulary for a nine-year-old, Harper told Channel Nine that "it's basically institutionalised racism".
"I just totally applaud her for taking a stand for what she believes".
"I tell you what - I'd give her a kick up the backside", Senator Hanson said.
While her parents have defended their daughter, the year four student was reportedly given detention by her school and later told that in the future she could either leave the building during the anthem or stand without singing.
"Shame on her parents for using her as a political pawn".
Controversial commentator Mark Latham spoke to 4BC about the matter, saying Harper's silent protest was a "behavioural problem" and she should be kicked out of school, while others blamed her parents for raising a disobedient child.
"I'm angry about this".
Queensland Liberal National politician Jarrod Bleijie called the young girl a "brat" on Twitter after the demonstration.
Former Prime Minister Tony Abbott also weighed in, telling Sydney radio station 2GB that Harper should "follow the rules", adding that it is "a sign of good manners and courtesy to stand for the national anthem".
"Stop the silly protest and stand and sing proudly..."
When she refused to do either, the school handed Harper a lunchtime detention for "blatant disrespect".
The Queensland Department of Education also said in a statement obtained by the local station that they had never suggested that Nielsen should be taken out of school for refusing to stand for the national anthem.
"State schools set out clear standards of behaviour that they expect from their students in their responsible behaviour plan for students", a spokesperson said.