Four digital examinations were affected – English Level 1 and 2, Media Studies Level 1, and Classical Studies Level 2.
"There were 5100 students entered for digital pilot examinations in 2017, with over 11,000 digital entries received across the six examinations offered," Gray said.
'We apologise to the students who have been impacted. We have been in touch with the relevant schools and most affected students should expect their results to be updated today.
"Although these are pilot examinations, this was unexpected. NZQA is taking immediate steps to change the marking interface and put additional controls in place to ensure this cannot occur in the future.
"NZQA remains on track to achieve its goal of having NCEA examinations available online by 2020, and will be working with schools and students to offer digital trial and pilot examinations in 2018."
The online exams in 55 schools were part of a pilot before the planned introduction of online exams for all subjects in the National Certificate of Educational Achievement (NCEA) in 2020 - a project NZQA calls the "future state".
One of the schools in the trial, Pakuranga College, said "the vast majority" of its 400 students who sat Level 1 English opted to do the exam online, and several in each class were given zero marks in error.
"We are concerned. There are a few showing up in most classes," said principal Mike Williams.
But he said he was confident that NZQA would identify and correct what went wrong, and urged the authority to go ahead with its plans to offer online exams to all NCEA students by 2020.
"I think it's a good vindication of the process they are using that you do trials, you go to pilots, you take the pilots to large scale, and you find out what goes wrong," he said.
He said students who did all their work through the year on computers naturally expected to sit exams with the same technology. But he said doing exams on paper would always remain an option for students who could not afford computers, and for those whose learning style was better suited to paper.
He said the glitches with Level 1 English had not stopped any students moving on to Level 2 this year.
"It's not a high-stakes thing. If it was Level 3 and widespread across a lot of things, it would be, but even there the majority of people are not always hanging on the last standard," he said.
Post Primary Teachers Association president Jack Boyle also urged NZQA to push ahead with its online exam plans with care.
"I think it's just teething problems," he said. "Go slowly, get it right. If you look at the phasing in of the pilots, then the trials, while there have been blips and issues, NZQA has gone back, they have had a real hard look at the problems to make sure there's integrity there."
