"The reason why I don't sing it or stand is because - Advance Australia Fair means advance White Australia", she said.
The school's principal had met with Harper and her parents to discuss alternatives to her protest, the Queensland state education department said.
He said Harper has shown "incredible bravery" in sticking to what she believes in.
Other prominent people, such as television host Georgie Gardner, praised the girl for her "strength and character", telling the BBC, "I do applaud her for considering the words of the national anthem, a lot of people just rattle it off and don't consider the meaning".
"Harper started questioning what was in the anthem, and we started talking with her about it".
Like the NFL gridiron players who have "taken a knee" during the U.S. national anthem in protest at racial inequity, these athletes were roundly condemned and ostracised by the sporting and political establishments.
"She's just asking for her opinion to be heard and for her feelings to be acknowledged, and for her to have an opportunity to take a stand on something she believes very strongly about". And yes, normally this is the place where I'd make a joke about them being a good intellectual match.
"And when it says 'we are young" it completely disregards the indigenous Australians who were here before us for 50,000 years".
Whether you think she's right or wrong - disrespectful or not - there is no excuse for belittling and bullying a nine-year-old child in front of the country.
Harper has the support of her "proud" dad Mark.
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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.
Kawana MP Jarrod Bleijie is adamant he would call any child a "brat", including his own, if they refused to abide by school rules.
"I'm angry about this ..."
"Stop the silly protest and stand and sing proudly your National Anthem".
"Rosa Parks refused to go to the back of the bus and Martin Luther King said "when that woman sat down I stood up", he said. "Suspension should follow if she continues to act like a brat", he said in a tweet.
Mark Nielsen, Harper's father, told Nine News his daughter was "very fearless", adding he had met with the school's principal but no agreement had been reached.
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.
Nevertheless, infuriated right-wing cultural warriors such as Mark Latham, are demanding the anthem be made compulsory in schools and are treating Nielsen's actions as some sort of crime that needs to be punished.