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Judge Andrew Becroft intervened in the case after the boy, 13, wrote to him following his suspension for his involvement in a fight.
The boy moved to the school last year as a directed enrolment, meaning the Ministry of Education ordered the school to enrol him after it initially refused.
The boy's letter, provided to RNZ by his mother, said his school would not let him participate in regular school activities and kept him in a room with a teacher away from but in full view of other children.
"I'm having a really hard time at school at the moment and hate being treated so differently to all the other students. I just want to make some friends and be treated like everyone else. I hate being bullied and laughed at because the teachers treat me differently and so do the other students," he wrote.