But the college argues it was in the right and, at a hearing in the High Court at Wellington today, sought a judicial review of the authority's decision.
The lawyer for the school board of trustees, Jessica Dickson, said the authority wrongly characterised the school's actions as a suspension on disciplinary grounds, which is not allowed.
It was instead a breach-of-contract matter between the school and the pupils, whose names are suppressed, and the authority was wrong to say education law overrode that.
The contracts signed by the boys' parents say the youngsters must abide by New Zealand laws, not take non-prescribed drugs and abide by Tauranga Boys' College rules.
Ms Dickson said the school board didn't accept the situation was handled unfairly too, in that two boys weren't excluded.
That decision was based on "circumstances, including their reaction to the incident and subsequent behaviour" and their risk to others and themselves and it was "nonsense" to say schools have no power over international pupils in these situations.
Jason McHerron, a lawyer appointed to help the court, said while Tauranga Boys' College might have wanted the matter to be a contract dispute, it instead suspended the pupils for disciplinary actions, which Ms Dickson agreed with unlawful.
"It's important your honour approach your decision with what really happened rather than what the school imagined happen or would like to have happened," Mr McHerron told Justice Rebecca Ellis.
The judge said she was concerned the school might have breached the boys' right to natural justice in its handling of the matter, including putting "essentially criminal allegations" to one boy without an interpreter, when the pupil didn't speak English very well.
"I struggle to see how a school can even enter a contract which governs people's private lives," Justice Ellis said.
She also wondered why the school didn't intervene about earlier allegations of one pupil drinking alcohol at a party.
The school board's application is academic to the three boys concerned, who were now back in Germany. But the school has requested guidance for the future.
The authority will operate in its present state until later this year.
The judge reserved her decision.