Cabinet papers show Education Minister Hekia Parata opposed a bail-out for Wanganui Collegiate.
Mrs Parata told her colleagues in October they should turn down an application by the school to become an integrated state school.
But Cabinet decided to agree to the application.
The decision saved the school from closure at the end of last year by increasing its Government funding from $800,000 per year to more than $3 million.
Radio New Zealand's education correspondent says advice from the Ministry of Education and the Treasury that Wanganui Collegiate should not join the state system was ignored.
Labour's education spokesperson Chris Hipkins says Mrs Parata is not in control of her portfolio and the big decisions are being made by other ministers.
But Prime Minister John Key says the decision to integrate Wanganui Collegiate was Mrs Parata's.
Mr Key says there had been differing views about what to do with the school but letting it join the state sector was the right thing to do.