Only one out of every 25 pupils in schools for those with behavioural difficulties or exclusions managed to gain passes in English and maths GCSEs this year, according to national data which also shows little headway being made in improving overall exam results.

Just 4% of those in England attending pupil referral units or similar alternative provision achieved grade 4s or higher in maths and English, while just 1.5% managed at least 5s in both subjects, the government’s favoured “strong pass” grade, with both figures being worse than the previous year’s results.

The national proportion of pupils in mainstream state schools achieving strong passes in compulsory GCSE maths and English fell slightly to below 44%. Despite a slight improvement in the number gaining 4s in the two subjects – equivalent to a grade C under the previous measure – more than one in three pupils were still unable to do so.

Geoff Barton, general secretary of the Association of School and College Leaders, said it was a tragedy that more than 190,000 young people could fall short of achieving at least a grade 4 in English and maths after 12 years of schooling.

“Every year this ‘forgotten third’ is a feature of our exam system, not by accident but because it is baked in by the mechanism used to distribute grades. We cannot continue to accept that one-third of pupils must ‘fail’ in order that two-thirds succeed,” Barton, a former secondary school headteacher, said.

“The government has raised the bar another notch by describing a grade 5 as a ‘strong pass’. Well over half of young people – 57% this year – do not attain this benchmark in GCSE English and maths despite all the effort they have put into their studies.

“It is a measure designed to raise standards but in fact risks leaving students feeling demoralised even though they have done really well.”

But while the overall results showed few positive signs, the school-level results calculated by the Department for Education (DfE) revealed some remarkable performances being made in improving pupils’ results at both GCSE and A-level exams.

Under the DfE’s progress measure – which compares GCSE outcomes with the same pupils’ results in tests at the end of primary school – three schools run by the Star Academies trust based in Blackburn showed the biggest improvements across England.

The Tauheedul Islam girls’ school in Blackburn run by Star Academies was the national leader for progress, with pupils achieving on average two grades higher in GCSE results than expected. But not far behind were two free schools established by Star Academies, the Eden boy’s school in Birmingham and the Eden girls’ school in Coventry.

A little further down on the progress table was the Eden Girls’ school in Waltham Forest and the Eden Girls’ school in Slough.

Hamid Patel, Star Academies’ chief executive, said: “For five of our schools to be ranked among the top 15 in the country for progress, with a number of others following closely after them, demonstrates that non-selective schools can compete with the very best in the country and make a real difference for our pupils.”

Michaela school, a free school in Brent that recorded its first GCSE results this summer, came fifth for progress with pupils achieving grades one and half times higher than their previous results would suggest.

“I am extremely proud of our children for what they have achieved and of our staff for the quality of their teaching. It’s also important to remember that school is not just about grades – I am equally proud of our children for how kind and considerate they are,” said Katharine Birbalsingh, the school’s head.

The national GCSE and A-level attainment tables were dominated by traditionally strong selective grammar and private schools, with three selective state girls schools topping the GCSE tables, and the independent St Paul’s girls’ school at the head of the table of A-levels by average points.

But a selective state sixth form college, King’s College London Maths school, came second by average A-level points, while its students’ progress was also high.

The DfE was keen to highlight the increasing proportion of pupils taking its favoured English baccalaureate suite of GCSE subjects, which nudged up to 40% this year. But school leaders say the government’s target of 75% take-up by 2024 appears unrealistic, because of the low number of pupils taking languages.