Auckland Primary Principals' Association president Frances Nelson warned the rapid population growth could put primary-aged children from the same families at different schools.
"Starting school is a really big deal for 5-year-olds, particularly if they're split from their siblings," Nelson told the Herald on Sunday.
Nelson said in many cases schools would have no choice but to turn away younger brothers and sisters of students until the ministry was able to "get more classrooms on site". But she said in some schools there was no room for new classrooms.
Green Bay Primary board of trustees chairwoman Gail Crann confirmed proposed zone changes would force some parents to find new school arrangements.
The school was struggling to accommodate its current roll of 582 and would cap the roll at 630 pupils when the enrolment zone came into force at the start of term four.
Without a "home zone", the roll could swell to 870 children in the next few years, said the ministry.
Crann said the Waitakere area was experiencing a population explosion as quarter-acre sections were carved up for multiple dwellings.
The area was also a destination for cashed-up families from central Auckland who were selling their homes for record prices and moving west for a mortgage-free lifestyle.
In recent years 253 Auckland schools have been forced to introduce a home zone: a catchment area from which they must accept students. Children living outside that area have to go through a ballot to secure a place at a school.
Under the pending changes Silverdale and Red Beach schools will also have to shrink their current home zones.
The Education Ministry said around 50 per cent of Auckland schools now had enrolment zones to manage roll growth.
The ministry was working with eight schools to implement new zones this year. Two more North Harbour primary schools had been asked to shrink existing zones.