, at least 200 secondary schools received unexpectedly low results in GCSE maths.
The figures have emerged from the PiXL (Partners in Excellence) Club, which worked with more than 400 schools entering pupils for GCSEs this year. Overall, it reports that schools serving disadvantaged pupils have been particularly badly affected by changes to GCSEs and the accountability system.
According to the organisation, the vast majority of its member schools usually improve the proportion of pupils achieving the benchmark of five GCSEs at grades A*-C including English and maths. But Sir John Rowling, chair of PiXL, said that the proportion had fallen in around half of the schools this year.
"There are many schools where this has had a devastating impact and they are often in disadvantaged areas, coastal communities.estate-type schools," he said. "There is despair, almost, among a lot of schools at what has happened. There are serious beliefs in many people that it is grossly unfair and disproportionately impacting on the hopes of disadvantaged, needy kids."
Sir John said that virtually all the schools that had missed the benchmark had received poorer than expected results for Year 11 pupils in GCSE maths. This trend was masked in the national figures - which show a 4.8 percentage point rise in A*-C grades - because of a reduction in early maths entries from weaker 15-year-olds, according to Sir John. "In reality, this Year 11 has been clobbered," he said.
Last week, Ofqual said schools had tended to enter only their most able pupils for maths at age 15. But the watchdog added that, nationally, results for 16-year-olds were up 3.9 percentage points at grade C.
Brian Lightman, general secretary of the Association of School and College Leaders, said that unexpectedly low GCSE English results were a problem in many secondaries. It did not appear that the results could all be accounted for by Ofqual's explanations of changes in entry patterns and the removal of speaking and listening from the overall English grade, he added.
"We are talking about hundreds of schools being affected," Mr Lightman said. "These results are so vitally important. The difference between a C and a D can make such a difference in career opportunities."
PiXL schools were less affected by the GCSE English results because most opted for the "stability" of IGCSE English, Sir John said. But results for the English literature GCSE in many PiXL member schools had "taken a nosedive", he added.
He said there was a perception among many secondary schools that grades in the subject were being "aligned" with English and English language GCSEs, where fewer pupils achieve good grades.
Sir John argued that PiXL schools had been hit by an intentionally tougher new geography GCSE and changes to league tables that meant vocational qualifications could only be judged as equivalent to a single GCSE.
"Schools with a large cohort of C-D borderline kids have ended up with masses of Ds, and some have seen a drop of up to 22 per cent on the five A*-C including English and maths benchmark," he said. "This year, just to hold your ground from where you were before might be regarded as a significant achievement, given the way everything has changed."
PiXL was formed to offer schools advice on how to secure the best exam and test results. But some tactics it has promoted, such as entering pupils simultaneously for two different English qualifications, have been condemned by the Department for Education as "cynical".
In 2012, controversy over English GCSE grades led to a group of schools, local authorities and teaching unions taking unsuccessful legal action against Ofqual and two exam boards. But Mr Lightman said there had been no discussions about similar action this year and he was also not sure that appeals against results would be appropriate for the schools affected.
An Ofqual spokesman said: "Standards were held steady this year. We were clear that this was the approach we would take in overseeing the awarding process, so that overall students were not disadvantaged, or advantaged, by the significant changes to the qualifications awarded this summer. But different schools were affected differently by the changes, depending on how big a shift the changes were for them and the approaches they took previously."