The schools have been warned by the Ministry of Education that charging for enrolment ballots is against the rules, and may create an inference of a guaranteed acceptance to the school.
This week it has emerged that two girls' schools are also engaging in the practice.
Epsom Girls' Grammar asks parents for a $20 "donation for administration costs" for all enrolment applications, while St Mary's College requests a $70 "non-refundable contribution to enrolment processing" - up from its 2015 fee of $50.
Mark Baker and his wife Dorothy applied for their daughter Caitlin, now 14, to attend St Mary's, and were charged $50 when they submitted their application for the 2015 school year.
"It was presented as a compulsory fee, it wasn't an option," Mr Baker, from Papakura, said.
He described the practice of schools requesting enrolment "donations" or "contributions" as "a rort".
"To be charged an admin fee for something that other schools are not charging an admin fee for, that's just kind of beyond the pale for me, disappointing."
Another parent who contacted the Weekend Herald said their family paid a $20 donation when applying for their daughter to be enrolled at Epsom Girls Grammar.
Epsom Girls' principal Lorraine Pound said the $20 sum was a donation, and not compulsory.
"We find that the majority of parents are supportive of that because they can see it reflects a real cost in administration," she said.
"It is certainly not a prerequisite to an application being received or proceeding."
The school had requested the same amount for all its applications for 10 years, she said, and she was confident parents did not feel it was a compulsory fee.
"It's very clear that it is a request for a donation."
The money went towards administration costs, Ms Pound said, adding there was "a lot of work associated with applications".
St Mary's College did not respond to requests for comment.
The Ministry of Education sent an Auckland-wide warning about seeking donations for out-of-zone enrolments after being alerted to the practices of Auckland Grammar and Cornwall Park District School.
The ministry's head of sector enablement and support, Katrina Casey, said it would be writing to Mt Albert Grammar, Epsom Girls' Grammar and St Mary's College to remind them about the regulations.
