Australian Christian College has now doubled down: Gary Underwood, the principal at Moreton, near Brisbane, has told mum Wendy Taniela that she must cut Cyrus' hair or he will have to leave the school.
Now his family is considering taking their fight to the Queensland Human Rights Commission because keeping the hair long is a traditional custom in their Cook Islands and Niuean cultures.
Cutting a boy's hair for the first time is a cultural rite of passage and Cyrus's family want to wait until he is 7. They have been planning the ceremony for the past three years.
Cyrus's father Jason Taniela's family is from Mangaia, and his mum's family is from Samoa and Aitutaki.
"They don't understand what it is coming to Australia," Mrs Taniela said.
Queensland Human Rights Commission spokeswoman Kate Marsh said they would try to resolve the issue if a complaint was made.
The Queensland Anti-Discrimination Act prevents discrimination on the basis of race at all educational institutions, including non-government schools.
The commission has warned the school's uniform policy could be in breach of the law, which prohibits indirect racial discrimination.
Mrs Taniela said both her and her husband's cultures - Cook Islands and Niuean - had hair cutting ceremonies.
"For us, we decided that it would be when Cyrus turned 7 that we would cut his hair," she told Redcliffe and Bayside Herald.
"We thought he'll have finished kindy and be able to understand what is happening.
"Traditionally, [on the Cook Islands] it [a boy's hair] is lovingly cared for by the boy's aunts and all the women and then there is a ceremony to cut his hair and traditionally the whole village celebrates."
Family in New South Wales, Queensland, Samoa, Niue and the Cook Islands, are saving money to come over for the ceremony in Sydney. More than 100 family members are expected.
Mrs Taniela told Cook Islands News she had met with the principal Gary Underwood who asked them to bring the ceremony forward.
"But this is a big cost, and we have other family commitments," she said.
"We don't all drive BMWs."
Mrs Taniela said it was a family tradition to tie Cyrus' hair in the morning.
"I spend more time on my son's hair than on my daughter's, because he's inherited the waves," she told Cook Islands News.
The school is the same one Cyrus' older sister Jaylia-Anna has been at for two years.
"Since last week, I have braided [Cyrus' hair] and tucked it up, above his collar. It is a fiddle. It takes me five minutes every morning, 10 minutes is he doesn't sit still."
She asked the principal if that was enough – but he said that was no longer his decision, it was a matter for the College's board.
Mr Underwood has now posted a statement on the school's Facebook page, saying he had spent time in the Cook Islands and was "an enthusiastic supporter of Islander people and their customs".
"He understands that cultural customs and respecting authority is also of huge importance and value to Pacific Islanders," the statement said.
"Respecting the College's policies, procedures and guidelines allows the College to be consistent across its many cultural groups.
"Further, to be consistent across all of the student body, all students are to conform to the board approved policies, procedures and guidelines which includes - 'Boys' hair is to be neat, tidy, above the collar and must not hang over the face. Extreme styles, ponytails and buns are not permitted'."
To support his assertion that he was "an enthusiastic support of Islander people", Mr Underwood also issued a photo of Pacific students performing a lunchtime show for classmates.
But the photo was issued without their permission – and Mrs Taniela said some of the girls in the photo were her own family, whose parents shared her concerns.
"For him to be so naive and to put up a photo of all those Islander kids – some of those girls are my nieces!"
Queensland Human Rights Commission's Ms Marsh said the state's Anti-Discrimination Act banned racial discrimination in schools.
"Cultural practice is generally accepted to be included under the attribute of race."
She said Australian Christian College's hair policy appeared to be indirect discrimination – meaning it would flout the law.