asked Ofqual chief executive Glenys Stacey how the watchdog knew the problems in maths wouldn't be replicated in other subjects, she admitted that extra checks would have to be carried out.
"We are looking ahead already to the new GCSEs in science and the individual sciences - where incidentally there is quite a lot of maths - and considering the sort of scrutinies that we will want to run alongside our usual processes," Ms Stacey said. "This is a new era of regulating."
Professor Alan Smithers, an assessment expert at the University of Buckingham, predicted that Ofqual and the exam boards would encounter problems with the science sample papers similar to those in maths.
He said Ofqual had been guilty of "circular reasoning" in the way it had tackled the maths standards issue, because of the pupils used in its research into the new assessments. "If you test [the new papers] out on pupils who have been taught the old GCSEs, then naturally they are going to find them very difficult," he said. "We may be lowering what we ask for in the new GCSEs to cater for people who have been taught under the old regime.
"If you are going to beef up the demand in a paper, then the sample you test it on needs to be people who have been taught at a more demanding level than the GCSEs at the moment."
Senior figures in the exams sector are understood to agree with Professor Smithers' analysis.
Ofqual `under review'
Sources at the DfE have already warned that Ofqual's entire role is "under review" because ministers have been "deeply unimpressed" by the watchdog's decision to stop practical work contributing towards GCSE and A-level science grades.
Education secretary Nicky Morgan said the move ran the risk of "holding back the next generation of scientists".
When sample papers for the new maths GCSEs were published last year, two of the exam boards (Edexcel and OCR) warned that a paper from a third (AQA) was too easy and would give it an unfair advantage in winning market share.
After the row became public, ministers made it known that they were "absolutely furious" that Ofqual had not done more to prevent a "race to the bottom".
The watchdog then began a major research project comparing standards between the sample papers. It included four separate studies and involved 3,865 pupils sitting the tests and comparisons from PhD mathematicians.
The results, published last week, confirmed that AQA's foundation paper needed to be made more difficult. But they also uncovered previously unnoticed problems with higher-tier sample papers produced by OCR, Edexcel and WJEC Eduqas; all three were told to introduce easier questions.
Teachers are unlikely to receive the new sample papers until the end of June - just three school weeks before they are supposed to start teaching the new qualifications.
Sue Pope, chair of general council at the Association of Teachers of Mathematics, said: "Why didn't [Ofqual] just listen to what teachers said in the first place - that the papers weren't comparable?
"It is a shame they have had to spend all this money to find that out. You would have hoped their experts would have sorted this out before things got accredited."
A school seeking stability
Continual reforms to GCSEs have prompted science teachers at Streatham and Clapham High School in South London to switch to IGCSEs from next term.
Sarah Fitzgibbon, head of physics at the independent girls' school, says that staff want to teach qualifications that are stable.
"When exam specifications are changed you are talking about thousands and thousands of pounds for new textbooks and everything else, whereas IGCSE just stays very, very constant for many years," she says.
"In the past, with GCSE, we have had to learn to deliver new pieces of coursework and now they are doing away with it altogether."