The authority told schools that exams should not be seen as optional, but Auckland principals said their students had been under a lot of stress from the city's long lockdown and forcing them to sit exams would be unreasonable.
Year 13 student Bethany said her school's principal had refused to confirm if students would get an unexpected event grade (UEG) if they skipped an exam.
"There are certain teachers who are being open about it and saying that NZQA has allowed us not to go to exams if we're happy with our UEGs but we have not heard it officially from the school that we can choose whether to attend or not," she said.
Bethany said some of her unexpected event grades were excellences, so it was impossible to get a better mark in the exams and she would be better off missing them so she could concentrate on her Scholarship exams.
Other schools in Auckland were taking a different approach from her school, she said.
"Their principals have said that you don't have to attend exams if you're happy with your UEGs, but our principal has not, so I think there needs to be one rule for everyone not different schools telling students different things," she said.
Hobsonville Point Secondary School principal Maurie Abraham said teachers at the school were sitting down with each student and discussing their unexpected event grades.
"If they think that's the result that they deserve then we're saying to them 'well you're a bit stressed out, there's a lot of anxiety, if you're happy with that then there's no real need for you to go along and sit the external examination'," he said.
"We don't want to subject them to unnecessary stress and anxiety around an external if they've already generated a good enough unexpected event grade."
The school's approach was within the rules and was especially appropriate for Year 13 students who had now endured two years of significant disruption, he said.
Sir Edmund Hillary Collegiate principal Kiri Turketo said the school was telling students "you do you".
The lockdown and pandemic had a big effect on many young people and giving them more choice around exams was having a positive effect, she said.
"I have seen the kids faces every day when they've come in, they look more connected, they're happier, there's this burden that's been taken off them because they can give up that anxiety about having to sit the exams."
Many students would still choose to sit the exams, but the unexpected event grade was a valid result for those who did not, Turketo said.
James Cook High principal Grant McMillan said teachers were telling students their unexpected event grades but also encouraging them to sit their exams.
"They know what they've got there, but we're also encouraging students to use the external exams to try and improve on that grade or lift what they've got in terms of an endorsement, merit or excellence," McMillan said.
Last month the Qualifications Authority wrote to schools to "reinforce the Government's clear expectation that students should attend NCEA exams as normal".
"The Government's intention is not for exams to be seen by students as optional, but to give students comfort that they will be able to receive a grade if there is a specific Covid reason that means they can't attend an exam," it said.
"The exceptions are those students who can't attend an exam due to Covid-specific reasons, such as isolating following medical or public health advice; being at higher risk of severe illness from Covid-19 and not fully vaccinated; experiencing significant personal or family related anxiety about exposure to Covid; or having an illness or injury which in other situations would normally require a derived grade."
The Qualifications Authority told RNZ valid reasons for using the unexpected event grade would be widespread and it did not want to increase the workload for schools.
"In line with this, while schools are required to have quality-assured the standard specific evidence they use to establish the grades, they are not required to verify the need to use an unexpected event grade for each student."
