Those in Auckland reported fewer problems and said wearing masks greatly reduced the likelihood students would catch Covid from one another or be required to isolate as a close contact.
Waimea College principal Scott Haines said schools' interpretation of the rules varied so much that some seemed to think there was no mandate.
"There are schools where principals are suggesting that mask use is not compulsory, it's recommended but they don't have to wear a mask in those indoor settings," he said.
Haines said his school enforced the mandate and staff had had to remind only a few students of the rules.
However, families could ask for an exemption for their child and Haines said figuring out who had a valid reason and who did not could be problematic.
"The issue that principals across the country, myself included, are grappling with is the expectation that we will support the mask mandate for students, rightly and properly so, but the tension that exists for us is identifying those students who are not wearing a mask and identifying do they have a valid exemption or not," he said.
Oropi School principal Andrew King said very few of his pupils had an exemption but he and other principals had noticed a growing number of applications.
He said some were based on bogus certificates or letters.
"They're sending in what they are calling official exemption letters using templates they've grabbed off the internet from various organisations," he said.
King said he did not accept those applications.
He said parents only needed to write to their school explaining the reason their child should not wear a mask.
"To decide whether or not that kid isn't worthy of that exemption is a tricky one because if their anxiety levels for example or wellbeing is being impacted because of the mask mandate, how do I argue that, even if they are a kid who's never had a mental health issue in the past," he said.
King said he expected the number of exemption requests would grow as more children and parents grew tired of the mask requirements.
Principals Federation president Cherie Taylor-Patel said the number of people seeking exemptions on doubtful grounds varied greatly from region to region.
"It seems to vary from region to region and from school to school. There might be a group of parents in a particular school area that have got hold of this exemption and they've taken it to their school. So I would say the issue is very variable from school to school," she said.
The Education Ministry said wearing masks was a requirement of a Public Health Order but no evidence was needed for someone to be considered exempt.
It said it was not aware of schools ignoring the mandate.