The heads' anger was expressed in an unusually sharp letter to John Patten, the minister, from John Sutton, general secretary of the Secondary Heads Association.
Earlier this month Mr Patten told the exam boards to respond to doubts about the consistency of marking and variations in syllabus at GCSE, following a critical report from Her Majesty's Inspectorate.
Mr Sutton said his association had not responded immediately, because it had not seen the HMI report. Now heads had read it, he said, 'I cannot convey to you the sense of anger and astonishment which has been expressed by our members, not with the report but with your response, and with the timing of it'.
He said that Mr Patten's criticism had devalued 'the very real achievements of pupils' who had just received their GCSE results, and undermined the general improvement in standards to which the GCSE exam had contributed.
The GCSE had proved 'without doubt one of the most successful of the many reforms introduced by your predecessors'. It had proved popular with teachers and pupils, and led to a 'surge of improvement in results and a very significant and continuing rise in the numbers of pupils remaining in full-time education post-16'.
Mr Sutton told Mr Patten: 'By undermining public confidence in what is a highly successful examination, on the limited evidence of long-standing technical problems inherent in the examining process, you have dealt a serious blow to the entire enterprise.'
The Secondary Heads Association also submitted its evidence to the teachers' pay review body yesterday, calling for an overall increase of 6 per cent.
Parents will end up dismissing the Government's Parent's Charter as worthless unless ministers set up simpler and more effective complaints procedures for schools, the National Consumer Council argues in a report today.
The council says that parents face a 'bewildering array' of different grievance procedures, which are anyway 'heavily loaded' in favour of schools and local authorities.
It suggests widening the local ombudsmen's range, enabling them to investigate complaints about opted out schools. Pupils aged 16 and over should be able to lodge a complaint themselves.
At present, parents have statutory rights to complain about problems with the curriculum, or religious worship, to appeal on school choice, exclusion from school, and special needs decisions. They can also appeal if the local authority or school governors are failing in their statutory duties, or acting unreasonably.
However, schools and education authorities are left to administer complaints on, for example, teachers' behaviour.
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