Logan Park High School principal Jane Johnson said an additional class of 30 pupils would be established next year, despite Ministry of Education predictions its roll would remain the same.
Kavanagh College principal Tracy O'Brien said his school would also create an additional class of year 9 pupils.
King's High School principal Dan Reddiex said his school's year 9 roll had increased from 146 pupils in 2010 to an expected 210 pupils next year.
The increase means he has had to create his third additional year 9 class in as many years.
Mrs Johnson said Logan Park High School had been working hard to market its curriculum and recent high academic achievement.
"Sometimes, for whatever reason, you change something and it works really well."
Mr Reddiex said word-of-mouth had been doing a great job of marketing King's High School to the parents of prospective pupils.
"It's some fundamental things. We have very high expectations of the boys, clear boundaries and accountability. Our values programme has been instrumental to the increase."
Mr O'Brien was surprised at the increase at his school.
Many pupils left primary Catholic education to go to intermediate and failed to return to the Catholic system, he said.
Next year, a significant increase in the number of these pupils would return to the Catholic system.
The school's maximum roll was 900 pupils and, based on the surge in year 9 enrolments, Mr O'Brien said the school would be "approaching" that limit next year.
However, Mr O'Brien said there was confusion about where the extra pupils were coming from.
Kaikorai Valley College principal Philip Craigie, Otago Boys' High School rector Clive Rennie, Bayfield High School principal Denis Slowley, Taieri College principal Christina Herrick and John McGlashan College principal Mike Corkery said their year 9 rolls remained static.
"We haven't nailed down the rhyme or reason for the increase yet," Mr O'Brien said.
"There's certainly not more kids about,"
Mr Reddiex agreed.
"The pool of students is basically static. It's not like we've got an increasing pool of year 8 students."
Mr O'Brien believed the increase could be partially explained by outside influences.
In the case of Kavanagh's year 9 surge, he said many of the extra pupils were coming from "out of town", some from as far away as Gore and Christchurch.
