Destiny Church has had an application to open a charter school declined by the Ministry of Education.
Church spokesman Richard Lewis said they were told on Tuesday evening the application to turn their existing private school into a charter school for years 1-13 had been turned down.
"The process has been ongoing all year, earlier last month we presented in Wellington and were a number of shortlisted applicants," Mr Lewis said.
"We hadn't had any communication until our letter on Tuesday. They had said they were very impressed with our application and the fact that we weren't a start-up model, but one that had been doing the work for the last nine, or 10 years."
Mr Lewis said church members were disappointed because the charter school model fitted with their educational vision - to lift the achievement of Maori and Pasifika students.
"All we can do is say all the best to the successful charter school applicants," Mr Lewis said.
Church leader Bishop Brian Tamaki voiced his disappointment on Twitter.
"If any 4 of the successful partnership schools chosen by Hekia Parata are weaker in critique than Destiny School then 'Discrimination' happnd."