Cullinane College principal Justin Harper said he was confident his students could make up their own minds.
"It's been a peaceful protest, and I'm very much in favour of peaceful protest," Harper said.
"I think Cullinane students are intelligent, articulate and worldly, and they'll be able to make well-informed decisions should they need to."
A flyer protesters were passing to students suggested that the vaccine was nothing more than an experiment, stating that side effects of the vaccine included cancer, stroke and brain damage.
According to the Ministry of Health, side effects of the Pfizer vaccine are minimal and include only minor issues such as pain or swelling near the injection site, headaches and fatigue.
Of the 1.2 million doses so far administered in New Zealand, only 6000 people have reported any side effects - equal to just 0.5 per cent.
Of those reported side effects, none was any of those listed by the protesters.
Whanganui Medical Officer of Health Dr Patrick O'Connor told the Chronicle, in relation to a separate story, that vaccine hesitancy was what would hold the world back from a return to normality.
"The greater our vaccine hesitancy, the slower will be our return to some form of normality - and there'll be more damage along the way."