A Ministry of Education scholarship giving students the chance to attend a private school has pulled Gloriavale's school from the list of options.
The Aspire Scholarship started in 2010 and is for students from low-income families going into Year 9.
The ministry pays up to $15,000 in fees for each student annually, and $1500 for course-related costs.
Gloriavale is a West Coast Christian community, which runs its own early childhood centres and school.
Earlier this year, a government inquiry announced it had uncovered a litany of allegations of sexual and physical offending at the isolated community, including that those living there were at an "ongoing risk" of being abused.
A senior manager at the ministry, Katrina Casey, said Gloriavale Christian Community School had always been on the list of schools compatible with the programme but that had been a mistake.
The ministry had removed the school because it did not accept students from outside the community and it did not charge fees, she said.
However, Ms Casey said she was unaware of any past scholars wanting to attend the school and no scholarships had ever been granted for it.
Three other private schools - Dilworth School, Ngā Kākano Christian Reo Rua Kura and Odyssey House School - were also ineligible because they were free or only accepted enrolments based on referrals.
The scholarship budget could support up to 250 scholars at one time, Ms Casey said.
"The number of scholarships awarded varies year to year depending on the number of exits as scholars complete their education. The ministry expects to be able to offer around 50 scholarships for 2018," she said.
Government research from 2012 showed most of the families of the 2010 recipients were still left out of pocket.
Ms Casey said the scholarship programme was reviewed last year and the ministry was considering making changes.