An exam board apologised for marking errors that could have affected GCSE and A-level grades after a whistleblower was suspended amid claims bosses told him not to inform schools.
In the wake of his claims, regulator Ofqual said it could not be certain that all pupils were yet in possession of the grades they deserved.
Channel 4 News said David Leitch, a senior supervisor at OCR, found wrongly calculated final scores in a hundred papers from last summer that schools had referred for checking.
A wider search found "hundreds more" mistakes by the same markers but Leitch claims he was instructed to inform only schools which had requested paid-for remarking, the programme said.
Dissatisfied with a review ordered by regulator Ofqual, C4 News reported, he last week emailed 30 schools directly to alert them to errors and has now been suspended by OCR pending a full inquiry.
Ofqual director of regulation Fiona Pethick said questions remained over the accuracy of marks.
Asked if she could be personally sure that no pupil still had a lower grade than they should, potentially affecting a university place, she told the programme: "I'm not satisfied yet.
"That's why we will be continuing to look into this matter and if we find OCR to be negligent we will take action."
A spokesman for the regulator added: "When this issue first arose, last year, we asked the exam board to carry out extended checks, identify the weaknesses in its processes and to put these right in time for the January exams. It appears that new evidence may have come to light."
OCR confirmed that Leitch had been suspended while it investigated.
Qualifications director Clara Kenyon said: "Mistakes can occur in a system where examiners mark using pen and paper on hard copy scripts. We apologise unreservedly to affected schools, students and their parents. This should never have happened."
A "formal and extensive investigation" of the initial problem had found 16 cases where pupils had received a lower grade than they should, she said - eight AS-levels, two A-levels and six GCSEs.
It resulted in the termination of four examiners' contracts and 78 others out of 13,000 - "almost all" teachers and ex-teachers with relevant degrees - being ordered to improve their performance.
But she insisted OCR had not been made aware of the existence of further errors.
"We were not told of the existence of these additional scripts with mistakes on them until schools contacted us," she said.
"This is of course a concern and we are processing them in the usual way and will make grade changes, if required, and inform schools."
The board was confident new safeguards would provide "a high level of clerical accuracy" in future, she said, pointing out that marks for three in four papers were calculated electronically.
All papers are due to be handled that way by 2014.
"Students taking exams both in the spring and this summer can be assured that mistakes of any sort will not be tolerated and we have taken the necessary measures to guard against them," she said.