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Thousands more London teenagers failed to pass enough GCSEs, putting their schools at risk of take-over following a shake-up of the exam system.

Almost 40 per cent of teenagers who took exams last summer failed to pass five A*-C GCSEs including English and maths, which is the minimum standard expected by employers.

It means an increasing number of schools could be classed as failing and risk being taken over by academies.

The exam results, published today by the Department for Education, are the first since sweeping changes were introduced last year.

Some headteachers branded the shake-up a “nonsense”, but supporters praised the new system for giving more accurate results and stopping schools playing the system.

Re-sits have been scrapped, sending schools that previously entered pupils for exams multiple times plummeting down league tables.

And IGCSEs - a qualification favoured by many private schools - have been stripped out, leaving top schools including Westminster, St Paul’s and Dulwich College branded with a zero pass rate in league tables.

Evening Standard analysis of the results show:

29,000 London pupils failed to pass five GCSEs including English and maths, an increase from 26,000 last year.

It means 38.5 per cent of London pupils failed to meet the basic “five GCSE” benchmark - up from 35 per cent last year.

40 London schools, where 25,000 pupils are taught, risk being classed as failing because fewer than 40 per cent of pupils passed five good GCSEs - which is below the government’s floor target. Last year in London the figure was 32.

But London continues to outperform the rest of the country, with a pass rate of 61.5 per cent compared to the national 53.4 per cent

30 per cent of London pupils gained the English Baccalaureate, which is awarded to pupils who pass GCSEs in five academic subjects, up from 29 per cent last year.

Education secretary Nicky Morgan said: “For too long pupils were offered courses of no value to them and schools felt pressured to enter young people for exams before they were ready.

“By stripping out thousands of poor quality qualifications and removing resits from tables some schools have seen changes in their standings.

“But fundamentally young people’s achievement matters more than being able to trumpet ever higher grades. Now pupils are spending more time in the classroom, not constantly sitting exams, and 90,000 more children are taking core academic subjects that will help them succeed in work and further study.”

Deputy Prime Minister Nick Clegg said some schools appear to have been “caught out” by the change in the way standards were measured, but believed they would quickly adapt to the new system.

He told LBC radio: “When you change the measurement of school performance, you always get a dip and change in the relative standing of schools, and I think what happens is that some schools just aren’t aware that the benchmark against which they are measured has changed, and then they adapt quickly and catch up.

“What we are seeing is partly a reflection not of schools slumping in the education they are providing kids, but that they are just not attuned yet to the new way in which they are being measured.”

The impact of the changes, along with a fall in English GCSE grades awarded last summer, mean the number of schools classed as failing nationally has doubled, from 154 to 330.

The Department for Education insisted that changes to the exams system will not affect individual pupils’ results, and that falling below the “floor standard” does not automatically mean a school will be taken over.

But private school heads said league tables have become a “nonsense” because of the decision to strip some qualifications out.

Richard Harman, headmaster of Uppingham school and chair of the HMC which represents 270 independent schools, said: “Several of the UK’s most highly performing independent schools and others offering this excellent qualification will now appear to be bottom of the class in the Government’s rankings.

“This obviously absurd situation creates further confusion for parents as they cannot compare schools’ performance accurately and transparently.

“Many HMC schools will continue to offer the iGCSE as experience tells us it is rigorous and offers a good basis for sixth form study. We know what works for our pupils and will always continue to provide a range of the best and most suitable courses, regardless of the vagaries of political decision making.”

Professor Alan Smithers of the University of Buckingham said: “Both the exams and the league tables are being made more realistic. They are giving more accurate information to pupils and about schools. This is a transition year which will lead to improvements. Naturally pupils and schools will look back to last years and make comparisons but they are not meaningful.”

A-level results were also published today. They show that the number of girls taking maths and physics has risen. The proportion of A-level entries in tough “facilitating” subjects has also increased. Facilitating subjects are those most sought after by top universities. Maths was the most popular A-level, accounting for 10.6 per cent of all entries - the highest since records began in 1996.