But High School is widely considered the superior school, and its NCEA results almost match those of the prestigious Wanganui Collegiate School. WHS often has a student waiting list, and real estate agents advertise houses as being within its zone.
While it is bulging at the seams, Wanganui's other state schools both have more than a 1000 spare seat capacity.
Ms Scott said from her figures it appeared the enrolment scheme had not had the desired effect.
The schemes were intended to prevent crowding, make sure students were chosen fairly and transparently and make the best use of the existing school network, she said.
However, this week MOE regional manager Jilly Tyler said mini enrolment schemes had been implemented to avoid overcrowding or the likelihood of overcrowding at a school.
An enrolment scheme assists a board of trustees in the management of the school roll.
A key component of an enrolment scheme was the "home zone". Students living within the home zone have the right to enrol at their local school, she said.
"The decision to introduce an enrolment zone was taken by a board of trustees and was supported by the MOE. There is a clearly-defined process to follow," she said.
Although it may sometimes not be possible for an out-of-zone student to attend their particular school of choice, enrolment scheme home zones are carefully created to ensure that every student can attend a reasonably convenient school, Ms Tyler said.
But a Wanganui man (who wished to remain anonymous) said the situation in Wanganui had glaring inequalities.
"The inequalities in student distribution in our local secondary schools is not a recent phenomenon. Nor is it accidental. It has been contrived by the deliberate actions of one school in particular within a climate of support by the Ministry of Education local office, who have encouraged, whether directly or indirectly, inequalities based on socio-economic backgrounds of local families."
And City College principal Peter Kaua said the zoning had divided on the basis of class with one school roll soaring and others struggling with student numbers.
The issue needed to be addressed at local government level and by the region's MPs because of the detrimental effect it was having on the community, he said.
"There needs to be some debate around the reasons why the WHS roll is soaring and the others are static or declining," Mr Kaua said.
Recent reforms announced for Christchurch, where some schools will merge and some will close, meant this was a community issue that needed to be debated, Mr Kaua said.
"Will this be the carbon copy of what is to be rolled out nationally?" he asked.
Mr Kaua made clear that his issue was with the zoning policy and not the board or staff at WHS.
WHS had established itself as the "school of choice" and as an educator that did some great work, however, there was a glaring imbalance in the student populations of local secondary schools.
Whanganui MP Chester Borrows said last week a review of secondary schooling was due for Wanganui, while Mayor Annette Main backed calls for a community meeting to discuss the controversial zoning policy.
Mr Borrows said enrolment rules and zoning for secondary schools "appear to be in a mess".
"We have a problem that needs sorting and sorting soon," he said.
"Many of us find it highly unusual that Wanganui High School is 106 per cent of cap, yet Wanganui Girls' College and Wanganui City College are vastly under-utilised,"he said.
Mr Borrows said the reality was that many people in Wanganui had been very dissatisfied with the way education and zoning had been set up.
"So it is high time the issue was looked at and something is changed."
Ms Main urged that a meeting between local secondary schools, the Wanganui District Council, the Ministry of Education, community leaders and MPs be called.
"I would support the idea of a meeting which has all parties present to discuss the issues arising from the zoning policy. The zoning is put in place by the ministry, and it would be good to get a better understanding of whether the original reasons for the current zoning were still relevant," Ms Main said.
City College principal Peter Kaua said the zoning in Wanganui was a community problem and the discussion should include everyone because of its detrimental effect on the community.
Though Wanganui High School is zoned, it has more than 50 per cent of the secondary school population enrolled, which leaves the other three schools battling to maintain numbers. The possible integration of Wanganui Collegiate could exacerbate that, he said.
Mr Borrows said it was incredible that many children drove past City College and Wanganui Girls' College to get to High School.
"There are legislated and regulated mechanisms to review enrolment procedures to prevent such huge disparities ... I believe that the configuration of secondary schools in Wanganui needs review in the future.
There are 1400 empty places in our schooling catchment."
Wanganui district councillor Michael Laws said the entire community needed to have the zoning debate.
"I have some sympathy for Peter's position. He is presiding over a school that is losing roll fast. We also have one school, Wanganui High School (WHS), with a roll that exceeds the combined roll of City College, Cullinane, Collegiate and Girls' College.
That is unique in New Zealand for one school to exhibit that dominance."
Students who were out of the WHS zone and wanted to attend the school but didn't fulfil ministry criteria were placed on a waiting list, which was then placed in a ballot.
However, since arriving in Wanganui five years ago, Mr Kaua said he'd had reservations about the way this ballot process operated and suggested there was a class component to the zoning.
"Well, I know that some students bus from Marton to attend WHS. Are they in the zone?" Mr Kaua asked.
This meant a student living in Marton could travel 40km to Wanganui High School but a student from Castlecliff could not, because they were out of the zone.
"If you look closely at the WHS zone, you will see that students from the lower socio-economic suburbs are excluded from the school," the principal said.
That had a significant social effect on the broader Wanganui community, Mr Kaua said.
"It's unhealthy because it reinforces the 'haves' and the 'have nots', which can't be good for any community locally or nationally, which is why we need to involve local government and our MPs," he said.
This was a community problem that should include everyone, Mr Kaua said.
The WHS enrolment zone was chosen in 1999 in consultation with other schools, Ms Scott said.
It takes in St John's Hill, Springvale, College Estate and parts of Gonville, and excludes Aramoho, Castlecliff and central city.
But the question remains.
Frequently asked by people in the community is how many WHS students come from outside the zone and how affluent or poor those communities are and why this is allowed to happen.