"An application from the Catholic Diocese for an increase in the maximum roll of John Paul College was declined recently because there is still surplus capacity in the Rotorua secondary school network," Ministry of Education acting head of sector enablement and support Susan Howan said.
Principal Patrick Walsh said they put forward a strong application with new grounds this year that he believed was not fully considered by the ministry.
"We were disappointed to be declined an increase again, particularly as our waiting list is becoming very large.
"Our grounds to increase our cap included Rotorua's growing Filipino community who are predominantly Roman Catholic, the 60 students we have coming here from Putaruru daily and the number of Aucklanders considering moving to Rotorua who want to send their children to John Paul College.
"In all these cases, they are not students that will then go to other schools in the city when we turn them away, they look to other areas - Hamilton or Tauranga.
"We have had to turn away Auckland families who then decline job offers in the city. This cap is not only bad for our school but for Rotorua as a city."
Mr Walsh said the ministry needed to be asking more probing questions about why parents were choosing to send their children to particular schools.
Meanwhile Rotorua Girls' High School has had a declining roll since at least 2010 when it sat at 886 students.
Principal Ally Gibbons said in a written statement to the Rotorua Daily Post that its declining roll could be attributed to disparities in students' genders.
"It's a complete misnomer to believe that the genders are born in equal numbers in any given year due to some demographic glitches often there's a disparity between the numbers of Year 9 girls and boys.
"However the fact that we have had fewer girls means that the girls we do have receive a really quality education that is uniquely tailored to their needs as young women.
"The opportunity to go to a girls only school is one that is the preserve of only the wealthy in other parts of the world. Isn't it interesting that New Zealand's few private schools are, in the main, single sex."
The primary schools with the biggest rolls for 2017 are Lynmore Primary School, Otonga Rd Primary School and Westbrook School with 667, 623 and 585 students respectively.
The smallest schools are Upper Atiamuri School, Rotorua Seventh Day Adventist School and Ngakuru School with rolls of 36, 45, and 50 students respectively.
At some popular schools, enrolment schemes and zones have been enforced to keep student numbers down but Western Heights Primary School principal Brent Griffin says with that comes the demolition of parental choice.
Mr Griffin said his school was currently sitting about 20 students over what he was comfortable with.
"Our roll is virtually impossible to track because a large portion of our student-base is transient, so it is constantly swinging in roundabouts. We usually sit around 460, which we are comfortable with, but we also have the enrolment scheme which prevents us growing to fit more
"If there's a school down the road that will fit more students, why would the ministry give a full school more space. It's finances, but with that we demolish parental choice and we see parents being forced to send their children to a school they are in zone for."
Ms Howan said the New Zealand education system still allowed for a "degree of parental choice" which sometimes resulted in students not being enrolled in their nearest schools.
"Where there is risk of overcrowding through enrolling students beyond a school's local capacity, we work with the school to develop an enrolment scheme with a defined home zone. This means that students outside of the zone can only attend if they are selected through a ballot. Enrolment schemes help schools under pressure and also schools with
spare capacity.