Western Heights Primary School will become a zoned school from next year, which means some pupils' siblings may not be able to attend the school.
The Ministry of Education held a meeting with board of trustees members last Friday to discuss the ministry's proposed enrolment scheme.
Board of trustees chairwoman Lucy Epapara said they had been fighting against the proposed enrolment scheme for a few months but the ministry told them during Friday's meeting it would be going ahead.
"We're not happy about it and the ministry know we are not but we will comply with them to get what we want in our proposed enrolment scheme.
"They are willing to negotiate which is good."
She said they would meet again on August 27 to discuss the number of students allowed at the school and how big the zone would be geographically.
Mrs Epapara said the ministry told them they would not be able to enrol over the top of another school, even though Aorangi School is only 400m down the road.
"We still need to negotiate about how the zone will work."
Rotorua mother Sarah Andrews, who has children at the school, told The Daily Post she feared the ministry's plans would mean her family members would have to move to another school to ensure the whanau stayed together.
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The school roll has increased from 295 in 2002 to 452.
At the end of 2010, the school approached the ministry asking for a new classroom as it did not have any space for small group teaching and to work with special needs pupils on a one-on-one basis.
Ministry officials told principal Brent Griffin a new classroom was not possible, and by the middle of last year the ministry told the school an enrolment scheme could be introduced.
Ministry spokesman Matt Radley has previously said zonings were introduced because of roll growth.
All students enrolled at the primary school will not be forced off the roll even if they live outside the school zone.
However, any new enrolments will go under strict criteria with first priority going to pupils inside the zone.