The pandemic has caused a 20 per cent slump in the number of NCEA credits schools have reported to the Qualifications Authority.
The authority said schools were cancelling or deferring some assessments and principals told RNZ they hoped their students would catch up before the end of the year.
The Qualifications Authority's deputy chief executive, assessment, Kristine Kilkelly, said it had expected a drop in reported results.
"The reduction in reporting appears to be mainly due to schools reducing and deferring their assessment programmes to later in the year in response to the disruptions from Covid-19, in line with the advice provided to schools in May and June.
"We expect the number of results reported to increase over the next two months, as assessment is completed prior to examinations."
The chairman of the PPTA's Principals Council, James Morris said 20 per cent was in line with what he had been hearing from other principals and he expected that figure would reduce by the end of the year.
"It will be interesting to see the final tallies, how much lower they are. I know, with the fact there's been the extension of when the exams take place, there's going to be a little bit more time at the other end for some catch-ups as well. So what I'm hearing is that there will be probably a greater amount of later credits going in."
Morris said schools were focusing on students who planned to leave school at the end of the year because returning students could catch up next year if necessary.
"One of the benefits of NCEA is that even if students aren't able to achieve it at the end of one year, they can always pick up the credits in the following year. I think a lot of schools have been really focusing on enabling the students who are leavers, so those who are possibly leaving at the end of level two but in particular level three, just making sure that they within this year will have the credits that they need for UE and level three as well."
Students lost five-and-a-half weeks of classroom time to the national lockdown and those in Auckland lost a further two-and-a-half weeks in the city's level 3 lockdown.
The principal of Mangere College in Auckland, Tom Webb, said despite the disruption the school's Year 13s were only slightly behind last year's rate of achievement, while other students had recorded about the same number of credits as last year.
"What we found, particularly coming out of the first lockdown is students being really engaged as they came back to school, really missing the time away from school and just wanting to get stuck in."
Webb said students had been a bit slower to return to classes following Auckland's level 3 lockdown, but they were showing the same motivation to do well.
He said the decline in results reported to NZQA might reflect a delay in reporting from schools rather than an actual decline in achievement.
He said his students' results were even better once learning recognition credits were added.
The principal of Albany Senior High School, Claire Amos, said her students had largely caught up after being behind.
"When we came out of the second lockdown it did look a little bit dire, it looked like we were really, really well behind because I think for a lot of students and a lot of teachers they were just about to do all their catch-ups from the first lockdown and then we headed into the second lockdown.
"But what we've actually found now is that with a real sense of flexibility being encouraged we're back to where we would be about this time of year already, so in a sense we've caught up."
Amos said the Qualifications Authority had encouraged schools to be more creative about how they gathered evidence that students had demonstrated the knowledge and skills required for achieving their NCEA standards.
"It was definitely a move towards that idea of gathering of evidence of learning rather than the traditional assessment events or tasks.
"It's actually encouraged our staff to approach NCEA in exactly the creative ways that we should have been doing all along."
Amos said with the addition of learning recognition credits, the school's students could end up achieving more credits than in previous years.