The government is targeting 638 schools, in which fewer than 30% of pupils achieve at least five good GCSEs including English and maths.
There are 27 secondary schools in Birmingham, 33 in Kent and 13 in Manchester facing this exams ultimatum.
The £400m standards drive, which will create up to 70 new academies, is to be unveiled by Schools Secretary Ed Balls.
The National Challenge, which was launched on 10 June, will require every secondary school in England to have achieved this GCSE benchmark within three years.
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