It is up to individual schools to decide if a student leaving class to attend a protest is an unjustified absence, principals say.

Thousands of young people on Friday joined rallies calling for action on climate change.

Secondary Principals' Association president Vaughan Couillault said although students had a right to attend protests, walking out of class could come with consequences.

"These young people who are taking strike action, they weren't in class, it wasn't a school trip. They were not in class.

"We knew where they were, and so you could say it's an explained absence. Whether you call it justified or not is up to you as a school member."

Associate Education Minister David Seymour criticised the rallies, saying students should be in school rather than protesting.

"If students feel strongly about sending a message, they could have marched on Tuesday when there was a nationwide teacher-only day, or during the upcoming school holidays. It has become far too common to sacrifice valuable learning time for other causes."

One student at a rally in Auckland told RNZ while her school disapproved of her extracurricular activities as an organiser, behind closed doors some teachers had expressed support.

Another protester, draped in a Palestine flag, told 1News Seymour was "a dick". Green Party co-leader Chloe Swarbrick said Seymour's view was "straight-up embarrassing".

Protest organiser Sophie Handford said if Seymour did not want students to miss school, then he needed to step up and treat the climate crisis for what it was.

Couillault said students could make their own choices.

"If the students want to rally and organise groups to express themselves, that's on them to do that. From a school perspective, we respect their right to do that. But there are consequences for that - you're not at school, you're marked absent - that's how it works."

Couillault said it was up to individual schools to decide if an absence was unjustified.

Read: Wānaka students climate protest.