Official papers show the Ministry of Education and the Treasury repeatedly told the Government not to let Wanganui Collegiate become a state school.
The former private school opened its doors as an integrated school this week - a change that increases its government funding from $800,000 to more than $3 million a year.
Documents show that the Ministry of Education warned the Government there are already 1400 empty places in secondary schools in the Whanganui-Rangitikei region, and integrating Wanganui Collegiate could hurt existing schools.
The ministry said the school has high rates of student achievement, but does little for groups the Government considers a priority, such as children from Maori and low-income families.
The papers provided under the Official Information Act say the school faces millions of dollars in building work and would have shut at the end of 2012 if it had not integrated.
Secondary Principals Association president Patrick Walsh says he is not surprised that the Government ignored advice from the Education Ministry and the Treasury, since it also ignored their opposition to allowing charter schools to have unregistered teachers.
He said most people would not have wanted Wanganui Collegiate to fall over, but now it is an integrated school there are issues of access that need to be addressed.
Mr Walsh said it has been suggested that some integrated schools ask for too much money in compulsory fees and voluntary donations and once private schools become integrated schools they should not charge larger fees.
Education Minister Hekia Parata on Wednesday defended the Government's decision to bring Wanganui Collegiate into the state education system against official advice.
Ms Parata dismissed criticism, saying advice came from officials and a range of government departments and the Cabinet made the decision.