While Leeds Metropolitan announced a new fee level of £8,500 for 2012, Reading said it would charge £9,000.
And Liverpool University confirmed that it is recommending to its council that the institution charge £9,000 to enable it "to continue to invest in and enhance the student experience as well as maintain its position as a leading Russell Group institution for widening access".
The council will meet on Wednesday.
It comes as a study by Research Fortnight magazine concluded that half of England's universities will charge maximum £9,000 fees, while only a few will set a level less than £8,000.
In a statement today, Leeds Metropolitan, a former polytechnic, said it was facing "difficult and tough choices" due to huge cuts in Government funding.
The university is one of the first of the newer universities officially to announce its fee levels.
Leeds Metropolitan's chairman of the board, Lord Woolmer of Leeds, said: "We are totally committed to providing a high-quality student experience.
"In the face of huge cuts in Government funding we face difficult and tough choices.
"We shall continue to secure cost savings but it is essential that we remain able to invest in high-quality university education and facilities for our students.
"We have a proud history of widening participating and will continue to support access into higher education and ensure that our students are successful at university and after they graduate."
Reading University said it has an "enviable record of providing a high-quality student experience" which it is "committed to upholding".
It added: "To sustain this level of support and investment for our students, in light of significant cuts in Government funding for universities, we will need to charge a fee of £9,000 across all our full-time undergraduate programmes.
"This will ensure we continue to provide our students with all the components of the highest-quality student experience, encompassing excellent teaching, pastoral and financial support, first-rate extracurricular opportunities and world-class facilities and student accommodation."
Reading will be putting together a package of support to help poorer students, it said.
According to Research Fortnight there is an increase in evidence that even low-ranked universities will charge high fees from next year.
As a result of the announcement by Leeds Metropolitan, and suggestions that St Mary's in Twickenham is likely to charge £8,000, the magazine is now forecasting average fees of £8,600.
After allowing for tuition fee waivers for poorer students, students could still be expected to pay £8,250.
"The consequences if this forecast is borne out will be severe, for the level of fees it suggests are significantly higher than the Government intended," the magazine said.
"For students, it means bigger debts. And for the Government, that may mean increased resentment from students and parents.
"For the Treasury, it means the threat of higher lending for student loans and an increase in the national debt.
"For the Department of Business, Innovation and Skills, it means warnings against 'clustering at the top end' have been ignored and increased pressure to dictate student numbers.
"For universities, it means lingering uncertainty as to how the Government will respond."
In total, 20 English universities have already declared their intended fee levels for next year, with the majority planning to charge the maximum £9,000. Almost all of these are among the most selective institutions.
The other universities planning to charge the maximum are Cambridge, Oxford, Imperial College London, University College London, Manchester, Warwick, Essex, Durham, Lancaster, Birmingham, Exeter, Surrey, and Aston.
Liverpool Hope has said it plans to charge less than £9,000, while Bishop Grosseteste University College Lincoln (BG) has said the fees for the majority of its courses will be set at £7,500.
London Metropolitan University has said it is likely to charge under £6,000 a year for many courses.
All universities planning to charge more than £6,000 will have to have their fees approved by the Office for Fair Access (Offa), and sign access agreements showing how they plan to ensure poorer students are not priced out.
MPs voted to raise tuition fees to £6,000 from 2012 at the end of last year, with institutions only allowed to charge up to £9,000 in "exceptional circumstances".
But so far, most universities are clustering around the £9,000 mark, with the most elite institutions leading the way.
This is set to cause problems for the Government which has based its future funding of universities on the assumption that most institutions will charge around £7,500.
Ministers have warned universities that if the majority set fees at or close to the maximum £9,000 then more funding for teaching may be lost.
A study by London Economics reveals that the number of students entering higher education could fall by around 45,000 per year if fees rise to an average of £7,500.
In its written submission to the Business Select Committee's inquiry into the future of higher education, London Economics warns that students will be £1.489 billion worse off under the new regime.
The average student will pay approximately £4,500 more for a degree course, it says, with around 84% of male and 67% of female graduates paying more.
Shadow universities minister Gareth Thomas said: "This analysis will confirm the worst fears of many - that the Government didn't think their plans through properly before forcing Parliament to treble tuition fees.
"The Government have clearly underestimated both the individual impact and the wider implications, on for example exports and postgraduate study, that the fees increase will have."
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