Brindabella Christian College has been reported to the tax office after it failed to pay superannuation to staff for nine months.
The Canberra Times understands the Independent Education Union ACT/NSW branch had been in discussions with staff about the unpaid superannuation.
The school assured the union the superannuation would be paid by Friday.
The Canberra Times sent questions to the Brindabella Christian College board regarding why the superannuation payments had not been made and when the staff would receive what they were owed but did not receive a response by time of publication.
Last year the independent school had 85 teachers and 46 non-teaching staff.
Separately, the college is fighting a decision from the ACT Civil and Administrative Tribunal in the ACT Supreme Court.
The tribunal ordered a car park at the Lyneham campus be closed and demolished as it was constructed in 2016 without a development application and went against the sublease and the zoning of the land.
The matter has been adjourned until next week. The school community is allowed to use the car park for a fortnight.
Brindabella Christian College increased tuition fees significantly this year, with fees increasing between 19 and 36 per cent depending on the year level.
Year 11 and 12 fees now cost $13,100 while Kindergarten to year 3 costs $9000 per year.
Parents were encouraged to pay the entire year's fees upfront before January 25 for an 8 per cent discount or by February 15 for 7.5 per cent off the cost.
The college had a $5 million debt with the tax office at the end of 2022, which was to be repaid in monthly instalments of $130,000.
The college's most recent financial statement showed at the end of 2022 the charity's current liabilities exceeded its current assets by almost $20 million, which the auditors said "may cast significant doubt on the Company's ability to continue as a going concern."
The college was involved in an Administrative Appeals Tribunal case to appeal a finding that Brindabella Christian Education Limited was not fit and proper to run a non-government school.
The federal Education Minister and college came to an agreement that the school would meet conditions relating to governance and financial management.
