More than 1,000 heads face the sack or having their schools taken over by academies' chains if they fail to improve exam performances.
Education Secretary Michael Gove is to write to local authorities and the schools' academy sponsors, giving them a tight deadline by which they must have produced an action plan for improvements.
This follows the revelation this week that 216 secondary schools have failed to reach the Government's "floor" target of every school getting 35 per cent of pupils to gain at least five A* to C grade passes at GCSE including maths and English. In addition, 962 primary schools where fewer than 60 per cent of pupils are fluent in English and maths in national curriculum tests are also on the list.
In his letter, Mr Gove spells out the following options for the schools: be taken over by one of the new academies' chains; work under a "superhead" recognised as "outstanding" by Ofsted, the education standards watchdog; or lose their headteacher permanently.
News of the clampdown emerged as Mr Gove confirmed the appointment of Liz Sidwell, currently chief executive of the Haberdashers' foundation – a group of academies in south London – as the Government's new Schools Commissioner.
Dr Sidwell is to encourage more schools to become academies and find solutions for under-performing schools. "I will not shy away from confronting failure and I will be honest when I don't think schools are improving fast enough," she said.
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