They were angered last week when the school told them they had entered pupils in the wrong algebra and graphing papers for NCEA level 1 maths due to "a computer glitch and human error".
Taieri College principal Christina Herrick took responsibility for the error and has worked to rectify the situation by liaising with NZQA.
Initially, NZQA said there would be sufficient evidence in the exam to measure pupils against the standard they should have sat and they would be given appropriate credit for the achievement shown at each grade - they could still achieve merit or excellence.
However, many of the 75 pupils affected were not confident they had done enough in the exam to pass, let alone get merit or excellence.
In a bid to resolve the situation, Taieri College allowed those affected by the exam mistake to sit unit standard papers this week.
Passing the unit standard papers allowed pupils to get the credits they would have missed out on, but only at an achieved level.
About 90% of those affected sat the unit standards, many of whom did not want to leave it to chance in case they failed some other standards.
But they were still unhappy about the lack of opportunity to gain merit and excellence.
In a rare move, an NZQA spokeswoman said the authority would now analyse the results from their exams last week and estimate likely grades based on other evidence such as practice exams.
The information would be used to substantiate final results.
"Hopefully, this multi-layering will help [pupils] get the best result possible. We're keen to see a win, win situation."
However, a parent of one of the affected pupils was still unhappy with the special consideration offered and said it was not an ideal solution for those who had "put all their eggs in one basket".
Many pupils might not have given their full effort in the practice exam because they had been told the exam was just that - a practice.
They had put all their effort into the end-of-year exam, she said.
"An ideal solution would have been for the kids to sit a special exam now. That would allow them to get merit or excellence."
Mrs Herrick gave assurances the incident had been dealt with and declined to say if anyone had been reprimanded for the mistake.
"I am constrained by employment law from discussing performance issues."
Board of trustees chairman Shane Boyle said the board was satisfied with Mrs Herrick's explanation for the mistake.
"It was a terribly unfortunate thing but unfortunately, mistakes are made from time to time. We're happy that Mrs Herrick took the right action. We're comfortable that the school is making the right changes to make sure it never happens again."
