Takeover by high-performing schools and academy chains, federation and closure are among the fates awaiting 216 secondaries singled out for Government intervention this week.

The schools failed to reach the new “floor target” of at least 35 per cent of pupils gaining five A*-C GCSEs including English and maths.

The Coalition is continuing the pressure on secondaries with low raw exam results, unadjusted for pupil intake, begun by Labour’s National Challenge.

Education secretary Michael Gove emphasised the collaborative side of the drive for improvement which would be on a scale “never witnessed before”.

“We will work with these schools - all of which have great potential and all of which will have staff ready to accept the challenge to improve,” he said. “We will provide them with extra resources. But on condition they work with us to develop tough, rigorous, immediate plans for improvement.”

Letters were sent to local authorities this week asking them how they intended to help the schools improve in a number of areas, including curriculum, staffing and discipline.

The Government’s new schools commissioner, Elizabeth Sidwell - former chief executive of the Haberdasher’s Aske’s academies federation - will review the plans and order further intervention where she thinks it is needed.

Brian Lightman, Association of School and College Leaders general secretary, said the fall in schools below the floor - down from 247 last year despite the target rising from 30 per cent to 35 per cent - showed the huge amount of work schools had already put in.

“The vast majority of schools still below the target are in the most challenging communities in the country,” he said.

“Most will already be working on measures to improve standards, but this does not happen overnight.”

Overall, the proportion of pupils gaining five A*-C GCSEs including English and maths rose by 3.6 percentage points to 53.4 per cent.

But heads are still smarting about the introduction of another league table measure - the English Baccalaureate (EBac), which requires pupils to gain at least C grade GCSEs or IGCSEs in English, two sciences, maths, history or geography and a language.

Only 15.6 per cent of pupils achieved the benchmark. But both state and private schools say its retrospective introduction, months after GCSEs were taken, is unfair.

Andy Burnham, Labour shadow education secretary, said he feared it would have a “devastating effect on morale” and “create a new generation of failing schools”.

Ministers said the “anchor measure” would always be five A*-C GCSEs including English and maths because it was “well known, reliable and robust” and allowed continuity.

The independent sector is particularly aggrieved as many of its schools scored zero on the EBacc because of a “technicality”.

A maths IGCSE from Cambridge Assessment qualifies for the measure. But the Government has left the equivalent Edexcel version out as it has not yet been accredited by Ofqual. The Headmasters’ and Headmistresses’ Conference says most of the 250 top private schools it represents use the Edexcel maths IGCSE and as a result their pupils automatically fail the EBac.

It has calculated that 76 per cent of its schools’ pupils would have achieved the measure if the Edexcel maths IGCSE had been counted.

The decision to leave out the Edexcel IGCSE from league tables also means many independents will continue to have noughts on the headline measure of five A*-C GCSEs including English and maths.

Newcastle Royal Grammar is one. Head Bernard Trafford condemned the decision as “bizarre”. “Government tables have always been misleading because they generally call for odd measures at the whim of ministers,” he said. “But this year they’re downright silly.”

Independent schools have long complained that they have been penalised by opting for more traditional O-level style IGCSEs that do not show up in the league tables.

The Coalition aimed to address the issue in June when it said state schools would be able to offer IGCSEs and that results would be included in league tables “as soon as possible”.

EBAC - AWOL EXAM

The Government has put a non-existent GCSE in its English Baccalaureate.

Ancient history is an option the Department says could add up to an EBac in this year’s league tables. But the Headmasters’ and Headmistresses’ Conference says no such exam was available last summer, a situation it describes as “ridiculous”.

An ancient history GCSE was introduced by the OCR board in 2009, but students will not be able to take the exam until June.

The HMC’s discontent has been compounded by the fact that a GCSE in classical civilisation, sat by thousands last summer, which represented an “almost exact” match to ancient history, was not included in the EBac.

The Department said ancient history was included because some pupils did take GCSEs in a single year.

• Original headline: Gove pledges support to bring GCSE strugglers up to scratch