The exam board AQA is to pay more than £1.1m in fines and compensation for a string of rule breaches, errors and failings in GCSEs and A-levels that regulators said could seriously undermine public confidence in the qualifications system.

Ofqual, which oversees school exams in England, said it had levied its largest ever fine on AQA after 50,000 appeals for exam papers to be reviewed or re-marked, spread across three years between 2016 and 2018, were carried out by AQA staff who had already marked the same papers.

The regulator also imposed a further fine and reprimands for other cases involving faulty exam design. In 2018 more than 100 students initially received lower French A-level grades, and a question used in practice papers was repeated in the GCSE English literature exam the same year.

In the most significant case, Ofqual found that AQA – the UK’s largest exam board, awarding more than 3m certificates each year – had overlooked internal warnings in 2016 and 2017 and failed to alert the regulator that re-marks were sometimes carried out by the same people who conducted the initial marking.

AQA will have to pay a £350,000 fine and give compensation worth £755,000 to the exam centres where the reviews or re-marks originated, as well as paying Ofqual’s costs for its investigation.

Ofqual said there was no evidence that students or schools had been affected, but warned: “These were serious breaches of conditions that are integral to the effectiveness and purpose of the system of reviewing marking and moderation.

“The failures therefore have the potential to seriously undermine public confidence in the review of marking, moderation and appeals system, and the qualifications system more generally.”

The investigation found AQA had failed to employ an appropriate workforce to administer appeals. Figures produced for Ofqual showed that AQA gained £217,000 in income from fees paid for the affected appeals, while it also saved more than £450,000 of “avoided costs” in lower staff and compliance expenses.

Mark Bedlow, AQA’s acting chief executive, described the failure as a “technical issue” that the charity has since fixed.

“Reviews of marking are only carried out by our best, most experienced examiners who are very unlikely to have made mistakes in their original marking – and, in the vast majority of cases, we’re talking about one isolated, anonymised answer from a paper being reviewed by the senior examiner who originally marked it.

“But reviews should always be carried out by a fresh pair of eyes and we’re sorry that, for a small proportion in the past, this wasn’t the case,” Bedlow said.

In the other incidents highlighted by Ofqual, AQA was fined £50,000 plus costs for a French A-level exam paper in 2018 for which markers penalised candidates who wrote in the correct words to answer a question, rather than choosing a corresponding letter.

Ofqual said AQA’s initial marking procedure was not fit for purpose. AQA later awarded higher grades to 135 candidates, and contacted the Ucas admissions service to ensure students did not miss out on university places.

But Ofqual criticised AQA for describing its response as a goodwill gesture, and said the exam board had missed a number of opportunities to correct its mistakes.