Most have been running sixth forms illegally for up to 30 years but have fewer than 100 pupils in each one. They asked Education and Employment Secretary Gillian Shephard to back them last year as the Government has committed itself to post-16 choice.
The sixth forms started largely in non-selective schools for students to resit exams. Government approval was not thought necessary and many have since become fully-fledged sixth forms.
Mrs Shephard told Kent education authority and the Funding Agency for Schools to hold talks. The FEFC was also told to investigate as it vets the need for all post-16 school or college courses.
The FEFC south-east regional committee decided this week that only six of the 40 were justified. Some failed the FEFC criteria on every count and some failed to make the case for a sixth form.
The FEFC said there would be no curriculum benefit. "The proposals did not offer an increase in choice and diversity," it said.
The LEAFAS inquiry has not ended yet. But senior figures in the Office for Standards in Education advised the inquiry that "much of the sixth-form provision is of doubtful quality".
Although schools may have close links with colleges and encourage student progression to FE programmes, some principals want many of the illegal sixth forms to be closed.
Nearly all of Kent's 120 secondary schools admit sixth-formers. The unofficial sixth forms were mostly set up in non-selective high schools. When numbers grew, they also offered a limited range of mostly vocational courses.
But Ben Thomason, principal of South Kent College, said post-16 education had been allowed to develop into a free-for-all. "There are a number of things we can do together with schools, but others are adamant that they want their own sixth form," he said. "Some of them are not sustainable."
The LEA and FAS are considering applications from 28 LEA and 14 grant-maintained schools to officially admit 17 and 18-year-olds. Two of the opted-out schools do not currently operate any sixth form.
And 10 schools which have held public consultations and submitted proposals to the Department for Education and Employment have had the applications put on hold until the outcome of the LEAFAS inquiry.
But the schools are adamant. "We are catering for students who wouldn't normally go on to any sort of further education," said Ramsgate School head Brian Lippitt.
Fewer schools are being granted permission to open new sixth forms in direct competition with colleges. DFEE figures recently showed the rate of sixth-form approvals has slowed significantly.
* Surveys of attitudes in the nine regions of the FEFC for England show decreasing anxiety in colleges over competition from school sixth-forms. The latest analysis from the North-west region shows a decline over 12 months from 46 per cent to 28 per cent of colleges who have cited competition as a threat to growth.