Former parents of Brindabella Christian College have made an application in the Federal Court for the charity that operates the school to be wound up on grounds of insolvency.
It comes after the school failed to pay the parents more than $17,000 and did not defend a matter at the ACT Civil and Administrative Tribunal.
However, board chair Greg Zwajgenberg said the debt was not paid because of an "administrative error" and there were no concerns over the college's solvency.
Hannah and Peter Griffiths had three children enrolled in the school's early learning centre and primary school over five years.
The parents made a lump sum payment of $10,000 to cover school fees while Ms Griffiths was on maternity leave and then moved to direct debit payments when she returned to work.
When the family moved interstate in 2019, the school claimed they owed money for school fees.
Ms Griffiths' calculations showed the $10,000 payment had not been applied to their account with the school and some direct debit payments had been duplicated.
The parents took Brindabella Christian Education Limited to the ACT Civil and Administrative Appeals Tribunal this year but the school did not respond to the claim.
The tribunal made a default judgement on March 22 which said the school owed the parents $17,487.35.
On May 2, the school was served with a statutory demand to pay within 21 days.
On May 24, Ms Griffiths filed an application with the Federal Court for the company to be wound up on the grounds of insolvency.
The application calls for liquidators to be appointed and for the costs of the plaintiffs to be paid out of the school's assets.
A court hearing is scheduled for June 30 where the school will need to prove it is solvent.
Mr Zwagjenberg said he expected the proceedings to be discontinued.
"Upon learning of the Federal Court proceedings, [the college] identified an administrative error that had prevented it becoming aware of the ACAT proceedings and statutory demand at the critically relevant times," he said.
"[Brindabella Christian College] immediately engaged with the applicants and expects the matter will be resolved informally with a discontinuance of the proceedings.
"As these discussions remain ongoing, [the college] does not intend to comment further other than to say that there are no concerns as to [the college's] solvency as a result of this matter."
The school has not yet published its 2021 financial report on the Australian Charities and Not-for-profits Commission website. The 2020 financial report showed the school made a $3 million loss.
The school had conditions placed on its approval after a protracted dispute with the Education Minister in the Administrative Appeals Tribunal.
The conditions included the school expand its board to at least five members and agree to a repayment plan for its multimillion-dollar debt with the Australian Taxation Office.
The school business manager was required to reconcile the relationship between debtors and fees in advance by June 1.
The school added two women to its board in April: Susan Power and Flora Lee.
The board chair previously said in a statement the school would be referring Education Department officials to the new federal anti-corruption agency and seeking to recoup costs from the appeal process.
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