Around two-thirds of English universities will charge the maximum £9,000 fee for some courses and almost half will do so across the board, according to new research.
Of 54 universities which responded to the BBC survey, 27 said they would charge the maximum for all courses. The overall average fee - where given - was £8,536.
Ministers have said that they expect universities to charge the maximum £9,000 only in "exceptional circumstances", and any setting fees at more than £6,000 are required to provide additional support, such as bursaries, to poorer students.
The growing evidence that the bulk of university courses will come in at more than £6,000 is not only a political embarrassment for the Government, but could cause financial difficulties for the Treasury, as ministers are committed to providing up-front loans to be paid back when graduates get well-paying jobs.
The BBC contacted all 111 state-funded universities in England that offer undergraduate courses, but not private universities nor those offering only postgraduate courses.
Nine out of 10 of the prestigious Russell Group universities said they would charge £9,000 across the board, as did the bulk of the 1994 Group, which represents other leading research universities. And there were wide variations in the level and type of support to be offered to students from disadvantaged backgrounds, with discounts ranging from £2,500 to £6,000.
Four of those questioned said that they expect courses to close as a result of the changes to funding arrangements, while one said that more than 10 courses would go.
All state-supported universities will have to clear their fees with the Office for Fair Access (Offa), which has the power to remove the right to charge more than £6,000 from any institution which is not doing enough to attract and support students from low-income households.
Shadow business secretary John Denham said: "The Tory-led Government has completely lost control of their fees policy. Future generations of students have been betrayed again and face even higher fees than the Government promised Parliament three months ago."
Universities minister David Willetts told the BBC News channel: "There are large numbers of special arrangements and there will be other universities and alternative providers - including further education colleges - still to decide. We believe that the average across the system as a whole will be significantly lower than that £9,000 headline figure."