There are about 1600 pupils eligible to receive the vaccine and it will also be offered to kaiako (teachers) and kaimahi (staff), bringing the total to between 2000 and 2300.
Whanganui District Health Board spokesperson Bruce Jones told RNZ's First Up pupils over 16 were able to consent for themselves and they had provided education on informed consent.
"If whānau did not want their students to be vaccinated at school, we've got a bit of a process where we can have a list of students that aren't to be vaccinated at school and we'll just make sure we honour their wishes that way.
"We just really need to know how many vaccinations are to be offered in that community so we can bring the right amount of vaccine in.
"We're taking a setting-based aproach, so the school community is the setting and anyone connected with that community would be able to be vaccinated if they're eligible."
Jones said some vaccinations would be administered today at Arahunga Specialist School in Gonville.
"The students come in from different satellite schools to Arahunga so we're also vaccinating their caregivers and the support staff that are with them.
"And then they wait in their classroom that they are familiar with for the 20 minutes or 30 minutes afterwards... they can do drawings or puzzles, talk to students or friends and then we're able to release them out of that area back to their normal day."
He said this rollout could provide a template for use of Pfizer on 12- to 15-year-olds once Medsafe approved that cohort.
"We've got the relationships with the schools ... we'll be able to talk to them about the roll-out for 12- to 15-year-olds when that comes online."
He said the main obstacle was fitting around the school timetable and curriculum but they were hoping for a smooth rollout.
"That's why we chose to talk to the schools this term and get all the logistics sorted... Term 3 is very busy for secondary schools and going in to term 4 with exams.
"With the programme in Whanganui, we're hoping to get that finished by hopefully the end of next term so we can be out of the schools for term 4."
Anyone wanting to support their tamariki during the vaccine administration could also do so, he said.
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Unbelievable that a vaccine (untested) is to be given to young people. Those in power have completely lost the plot.
Whanganui school students 16 years and over are set to recieve their 1st dose of the vaccinations from next term. My 85 year old mother hasnt had her 1st jab yet and has no idea when its due. Work that out. What happened to the vulnerable elderly spoken of so much?.