The Government ignored advice from the Ministry of Education and the Treasury that the private Wanganui Collegiate should not become a state integrated school.
Information obtained by Radio New Zealand under the Official Information Act shows the ministry told the Government that integration would hurt existing state secondary schools in the area.
In October last year, Whanganui MP Chester Borrows told the Chronicle a review of secondary schooling was needed, and he described enrolment and zoning in the city as a "mess".
There were 1400 empty places in the catchment and Wanganui High School was at 106 per cent of its roll cap.
"We have a problem that needs sorting and sorting soon," Mr Borrows said.
Education Minister Hekia Parata announced on November 2 last year that Collegiate had been successful in its bid for integration. She said the school had been working toward integration for more than two years and was one of the top performing schools in the region.
Integration came with a funding increase from $800,000 a year to more than $3 million.
Green Party education spokeswoman Catherine Delahunty said the Government had more than tripled the amount of money it gave to the school, while closing schools in Christchurch.
"It is yet another example of privileging the privileged, while everyday New Zealanders suffer," she said. "The decision to hand out more cash to Wanganui Collegiate is a slap in the face for Christchurch students, parents and teachers, who are desperately trying to save the schools that helped them through the traumatic experiences of the last two and a half years."
In June last year, Wanganui Collegiate boasted low class sizes in advertisements - after the Government ditched plans to make $43 million savings a year by increasing class sizes.
The school has faced financial strife since 1991, when it made the move to become co-educational.
It sold the land and buildings that housed St George's preparatory school, valued at $3.1 million.
Last year, there were 518 students over the two schools and this year fees will increase by more than 10 per cent.
Outgoing Wanganui Collegiate board chair Tam Jex-Blake wrote to parents in December last year, saying they would have to pay more.
In 2011, then Education Minister Anne Tolley gave Wanganui Collegiate more than $800,000 in extra funding, while the school's application to become a state integrated school was negotiated.
At the time, Wanganui Girls' College said there was not enough funding in the region to support the current regime of public schools.APNZ