The commission has also recommended the ACT government amend the Education Act 2004 to ensure safeguards apply to all decisions to not enrol or re-enrol students.

Brindabella Christian College did not allow the brothers to re-enrol at the school at the beginning of 2020 after their parents, Jodie and Aldrin Jayatilaka, approached the school board about instability the high turnover of teachers.

The school advised the family that the boys, due to enter year 9 and year 12, were not to be re-enrolled because the parents had "displayed outward displeasure at the administration of the school" and they had "encouraged others to also find issues with the way in which the school and the education is administered in a way that has created an unhealthy environment of anger and disunity".

In a final report published on Friday, the ACT Human Rights Commission came to the view that the decision to not re-enrol the students was inconsistent with four of the ten National Principles of Child Safe Organisations and the school did not appropriately provide a service for children and young people.

The commission found the school did not abide by procedural fairness when it decided to exclude the students without any opportunity for them to participate in the decision.

Mrs Jayatilaka had made a previous complaint about the school and its board to the commission in September 2019 after her daughter was pulled out of class and questioned about her feelings towards board members.

The commission found the school did not allow her sons to be enrolled because she had made the previous complaint, which was contrary to section 98 of the Human Rights Act.

The commission recommended the school review its enrolment agreement and complaints policy to ensure they were consistent with the National Principles of Child Safe Organisations, the Discrimination Act 1991 and the ACT Education Act 2004.

It recommended the school provide a report of these reviews to the ACT Education Directorate and the federal Education Department within six months.

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The commission also called for the Education Directorate to work on its registration standards and oversight mechanism of non-government schools to ensure it can investigate complaints and concerns about non-compliance with registration and provide a report to the ACT Education Minister within 12 months.

"The commission notes the ACT government, as a public authority, has obligations under the Human Rights Act 2004 to act consistently with human rights, including the right to equality before the law, freedom of expression, and the right to education," the report said.

"This includes taking steps to protect individuals from having their rights breached by third parties."

A spokeswoman for Education Minister Yvette Berry said the ACT government would consider the recommendations and respond in the required timeframe.

"Non-government schools can establish their own enrolment guidelines. While section 105 of the Education Act 2004 ensures procedural fairness where an exclusion is based on a student's behaviour, this does not prevent non-government schools from excluding a student for other reasons."

The spokeswoman said the ACT government was undergoing a review of the Education Act 2004 including the regulation of non-government schools.

Mr and Mrs Jayatilaka said they were relieved to read the findings and supported the recommendations.

"Parents have been sounding the alarm at Brindabella Christian College for years, asking for help to rectify governance issues and the unaccountable board structure which has impacted the learning environment and welfare of hundreds of children.

"These findings seem to fall short of addressing their governance structure and there appears to be no penalties applied to the school board for their actions.

"We're hoping these findings are the beginning of enduring changes at Brindabella."

Brindabella Christian College was contacted for comment.