Under Ministry of Education guidelines masks are not mandatory, but are highly recommended for over-12s in school during Alert Level 2.
Kaikorai Valley College principal Rick Geerlofs said about 20% of pupils were wearing masks yesterday, and fewer pupils would probably wear masks as the days went on.
The school was encouraging pupils to wear them, but it was important not to press the matter and end up in conflict with the pupils, he said.
"It’s really important that we support them in terms of their return."
Special needs teacher Gill Whyman said almost all her pupils had chosen to wear masks and they were doing tasks that helped them feel more comfortable, such as drawing masked-up self-portraits.

In Tapanui, Blue Mountain College principal Lindy Cavanagh-Monaghan said staff were leading by example and wearing masks whenever it was practical, but she expected the number of pupils wearing them to drop as time passed.
"Teenagers will be teenagers", and if something did not fit the socially acceptable "vibe" there was no forcing it, she said.
Principals in Dunedin agreed with that assessment.
Bayfield High School principal Mark Jones said he anticipated a small few would keep up with their mask wearing.
A lot fewer pupils were wearing masks than Queen’s High School principal Barbara Agnew had expected, but they were doing so in tight spaces, such as the canteen queue.
In Southland, Verdon College principal Jarlath Kelly said mask-wearing was an individual choice and some pupils had chosen to wear them.
Those who had worn masks might have had vulnerable family members or health concerns and that choice would be respected, he said.
Maniototo Area School principal Joe Ferdinands was optimistic mask wearing would increase.
Not many of the school’s older pupils had worn masks, but he expected more to as they saw other pupils and staff wearing them.