Figures showing how many pupils go to schools out of their area highlight the problems with the zoning system, the Secondary Principals' Council says.
Ministry of Education data provided to RNZ News show about 81,000 primary and secondary pupils are attending schools they are not zoned for.
The figures show that dozens of schools are taking more than half their pupils from areas that don't fall within the school's zone.
In some schools, more than 75 percent of the students were from an area outside the enrolment scheme zone.
Overall, about 11 percent of children go to schools with an enrolment scheme that places them out of zone, with that figure jumping to 15 percent in the Auckland region.
Not all schools have zones, without about half the country's 700,000 school pupils attending schools without enrolment schemes.
Some of the highest out-of-zone populations were at single-sex city schools, including Hamilton Boys' and Girls' High Schools, Palmerston North Boys' and Girls' High Schools, and Southland Boys' and Girls' High Schools.
Senior ministry official Katrina Casey said in a written statement that was because single-sex schools tended to draw students from across a wide geographic area.
The ministry believed 11 percent was a reasonable proportion, Ms Casey said.
The ministry had confidence in enrolment schemes and the vast majority of families abided by the rules.
"In our experience individual school boards of trustees do a good job of managing their enrolment schemes and investigating any concerns," she said.
However, Secondary Principals' Council president Allan Vester said the data confirmed deep-rooted problems with the zoning system.
Many of the schools taking large numbers of out-of-zone pupils were schools that had physically expanded during the 1990s but now were unable to fill their rolls with local pupils, he said.
That was due to a complex combination of factors, including parents sending their children to schools in other areas, which created a flow-on effect for their local school; areas no longer being affordable for school-age families to buy in; and a current dip in the school-age population, Mr Vester said.
"It's something we've been talking about for a long, long time, in terms of ... the increasing divergence of the low- and high-decile communities," he said.
"We've got in place ... a programme of choice which is now creating significant problems around resourcing."
However, the zoning system was now so entrenched that it would be difficult to scrap or make major changes to it, Mr Vester said.
The 11 percent figures seemed on the low side, he said.
If primary schools, where rolls were largely made up of local pupils, were removed, the out-of-zone proportion would be much higher.
Canterbury University education specialist Dr Liz Gordon said she was surprised that a quarter of all primary schools had an enrolment scheme.
She said top schools were getting bigger and becoming more viable while smaller, lower decile schools were doing the opposite - and the current zoning policy perpetuated that trend.
People were 'choosing up' socially in particular markets, Dr Gordon said.