The board also said the personal grievance was filed outside the 90-day period.
It said Mr Roy had similar proceedings before the Human Rights Tribunal and matters of religion were outside the authority's jurisdiction.
Mr Roy said he was under duress and had no access to legal advice at the time the record of settlement was signed.
The authority said there were factual disputes that could only be decided at a hearing, which is to be held in May.
Tamaki College a public school in Glen Innes. Its 700 students are mostly from Pacific Island and Maori backgrounds.
The chairman of the school's board of trustees is listed on its website as Alfred Ngaro, who is also a National List MP.
Tamaki College principal Soana Pamaka said the school had no comment to make, as the matter was still before the authority.
She also wouldn't comment on the school's policy on religion.
Staff at Mr Ngaro's office said he was busy in meetings today and would not be able to return calls.