Principals says low-decile schools are just as good but many parents are increasingly opting to send their kids to schools in more affluent areas.
Schools in poorer communities are shrinking as local families abandon them for those in wealthier suburbs.
A Herald analysis of roll numbers for 565 schools in greater Auckland shows that while a population boom has doubled the size of some schools in 10 years, some in poorer areas are haemorrhaging students and attached funding.
In the past 10 years the overall number of students in decile 1 to 6 schools has dropped, whereas the number attending decile 7 to 10 schools has increased.
A school's decile ranking is used to determine how much public funding it needs and is arrived at by scoring socio-economic factors such as students' household income.
Decile 1 schools are the 10 per cent of schools with the highest proportion of students from low socio-economic communities, whereas decile 10 schools are the 10 per cent with the lowest proportion of these students.
While officials point to a number of factors contributing to the growth divide between decile bands, schools say too many parents mistakenly think decile is related to the quality of education a school provides.
• Auckland classrooms at bursting point (+infographic)
As a result, the challenges facing schools in poorer communities are worsened because the more well-off students in their area go elsewhere - deepening the social divides between haves and have-nots.
Roy Lilley, principal of Henderson's Bruce McLaren Intermediate since April 2010, said the phenomenon was visible to anyone catching public transport in Auckland's west.
"That railway line now, kids from right outside of Henderson and Swanson can go all the way down to Avondale, Mt Albert, Auckland Grammar, St Peter's," he said. "Get on a train in the morning and you will see kids in their hundreds and in their thousands pouring out of West Auckland to go to all those schools."
Mr Lilley said that while Bruce McLaren was decile 3, it and other schools in the west stacked up based on student progress. "I can't understand why they would take kids away ... there's no need, it's just a perception thing, and it's a hard perception to break."
In Auckland's south, decile 1 James Cook High School draws few students from the Wattle Downs suburb, despite being the nearest secondary school. Many students from the area, which is affluent in comparison with James Cook's other catchment suburbs of Clendon and Weymouth, travel each day to East Auckland, said Vaughan Couillault, James Cook's principal. That was disappointing as his staff were "fantastic".
"There are a number of families in Wattle Downs that have given us the opportunity, and their children have really benefited from the education that we've been able to give them.
"Again, it's that confusion about decile rating and quality."
Mr Couillault, who took over at James Cook in 2012, said that confusion was recently demonstrated when a family member asked him how he could improve his school's decile rating: "I said, for God's sake it's nothing to do with us - I can't."
The Government itself has criticised the decile system. In an interview this month Education Minister Hekia Parata described it as a "blunt instrument" and said she wanted to explore other systems.
But her comments indicating she would consider a more performance-related funding regime alarmed unions, who say the Government's focus on student achievement data furthers parent misperceptions about school quality.
Last night, Ms Parata rejected that criticism and said publishing student achievement data "shows where we are doing well and where we might do better". "It provides a starting point for communities and schools to identify where weaknesses lie and how outcomes can be improved."
Ms Parata said the ministry published a checklist of factors parents can consider when choosing a school. Parents took into account many factors including Education Review Office reviews and recommendations from other parents.
Earlier, Associate Education Minister Nikki Kaye said the Herald's figures showing a decline in students at lower decile schools could not be directly attributed to a rise in numbers at higher decile schools.
They did not account for 63 schools that had closed or opened since 2003, and many schools' decile rating would have changed in that time.
Roll change could be for a number of reasons including internal migration and immigration, Ms Kaye said, and pockets of growth in Auckland were typically high decile.
Allan Vester, chairman of the Secondary Principals' Council and head of Edgewater College in Pakuranga, said those factors would influence the figures. But previous research and the amount of traffic on the road around school closing and opening hours showed some families avoided lower decile schools.
"The pattern is absolutely clear. Almost no students will travel out of a higher decile school zone to go to a lower decile school. The movement is almost always in the other direction."
Because some funding is attached to student numbers, the decile roll gap had implications for a school's budget. Another consequence was an increasing polarisation between haves and have-nots.
"When the Prime Minister and I went to school kids did generally go to their local school and mixed with whoever turned up," Mr Vester said.
"Now there is a lot of time and energy expended getting children into a good school which unfortunately in many people's minds means higher decile."
Changing such attitudes was hard, he said. The idea that decile is a de facto measure of quality was well established, and the numbers were a favourite of real estate agents.
"Long-term, the only thing which will slow the trend is a system that ensures that every school is a great school. Even that won't do the whole trick because a significant part of the decile drift is really social drift," Mr Vester said.
"Parents are looking for a good education but also for a chance for their children to be with other kids they would like their children to be like."
This year saw New Zealand's first five charter or "partnership" schools open, under a confidence and supply agreement between the Act Party and National.
Act education spokesman David Seymour told the Herald the new publicly funded but privately run schools were a response to struggling state schools that were correctly rejected by many parents.
It was patronising to suggest that parents based the decision of where to send their children on the decile system, Mr Seymour said.
"There is a shortage of supply of good schools ... parents and children are scrambling over each other to get to a limited supply of schools that they find desirable.
"I just don't buy the argument that, 'oh, the parents just don't know, there are good schools but they don't know to go to them'."
In the past five years 11 new state schools opened in Auckland, with $276 million spent on them and 330 classrooms to mop up roll growth.
A Herald interactive graphic shows how the rolls at 565 schools in greater Auckland have changed over the past decade and that many lower-decile schools have shrunk.
There can be a range of factors behind declining rolls, and some schools will deliberately downsize or remain near capacity. The ministry actively amends school zones to cope with population changes, but frustration remains.
The roll at Wesley Intermediate in Mt Roskill, a decile 1 school, has fallen 25 per cent since 2003 to 123 students last year. Principal Nigel Davis said the extension of the nearby Southwestern Motorway had affected his catchment area, and people had also left the suburb to find work. The school's zoning was also frustrating.
"Our back field, if you live on the other side of our fence, you are in zone for Roskill Intermediate."
While losing children to higher decile schools was not a major problem, Mr Davis said when he asked parents why they avoided their local school sometimes the reason given was to do with ethnicity.
For Mr Couillault of James Cook, it was important for a school's roll to reflect the make-up of its community.
"I want that for my community ... you experience a cross-section of the society in which you live."
Roll divide costs us all: researcher
The roll growth gap between schools in rich and poor areas is a national issue, a leading education researcher says.
A NZ Council for Education Research survey of secondary schools, which included 1477 parents, found that 40 per cent of parents sent their children to a secondary school that was not their closest school - usually to a higher-decile school.
Nationally, the number of students in decile 1 to 3 schools declined by 12 per cent from 2000 to 2011, while the numbers in decile 8 to 10 schools grew by 23 per cent.
NZCER chief researcher Dr Cathy Wylie said the survey found almost all schools with enrolment zones - intended to check the over-growth of some schools at the expense of others - took students from outside their zone. Forty-one per cent of schools with enrolment zones drew a fifth or more of their roll from outside their zone.
"The costs of competition between schools are there for students - international evidence suggests that even socio-economic mixes in schools are beneficial for learning," Dr Wylie said.
"But it's also a cost on the public purse if it means empty buildings in some schools, and pressure to add more buildings and amenities in others."
Further data on primary school competition for students will be available when NZCER releases an overview on its 2013 national primary survey.