The Vice Chancellor,Mike Fitzgerald, resigned after the report by the universities watchdog, the Quality Assurance Agency for Higher Education.
He will be replaced by an acting vice-chancellor, Sir William Taylor, who is currently President of the Society for Research in Higher Education.
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In a statement, Mr Fitzgerald said he had resigned "in the interests of the university and its continuing development".
The university, based at campuses in Ealing and Slough, had invited the quality agency to investigate allegations of insufficiently rigorous standards, following an industrial dispute over plans to merge departments and introduce a complex system of course modules, and delays in marking students' work.
Thames Valley had previously gained a reputation for offering unusual courses, including kite-flying and rock music.
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This is the first time that the agency has given such a warning on standards and in response the Higher Education Funding Council for England is planning to work with the university on implementing an 'action plan'.
The damning report said there was evidence that the university "might have lost sight of some basic principles of quality assurance which should be commonplace in an institution with independent degree-awarding powers".
"If you're going to have new, progressive ways of making higher education accessible, you have to make sure they're properly managed," said John Randall of the quality agency. "And that was where the failure was."
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The quality of teaching is not in question. But students are worried that the outside world will get the impression from what has happened that Thames Valley degrees are not worth anything.
The university's Chair of Governors, Sheila Forbes, stresses that the report is not about the standard of degrees and that it was the governors themselves who had invited in the quality agency to help them improve a situation they knew to be unsatisfactory.
"We are going to work very hard internally on the action plan that the funding council have asked us to put together," she said.
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"And we are going to work very hard outside with students, with employers, with colleges and schools with whom we already have lots of links and lots of partnerships.
"We provide a wide range of courses which meet the needs of students in this region."
Among the problems facing the recovery team will be a 30% shortfall in this year's student intake, which will have implications for funding.
Part-timers
The university, which has 28,000 students, has pioneered a policy of "mass participation in higher education".
The majority of its students are female and mature, with 65% on part-time courses.
The Higher Education Minister, Baroness Blackstone, backed the quality agency's criticisms, saying "the taxpayer expects value for money from the £6bn a year spent on higher education".
"Standards are in jeopardy at Thames Valley University," she said. "This is a serious matter and we expect the governors to take firm and decisive action to address this failure."
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Thames Valley University
Higher Education Funding Council for England
Quality Assurance Agency for Higher Education
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