Even after fee waivers are taken into account the average fee will be £8,161, compared to the figure of around £7,500 envisaged by ministers.
Data released by Offa as it announced the approval of access agreements for 139 universities and colleges also show that one in three higher education institutions will charge £9,000 for all courses, while two thirds will charge the maximum for some.
Sector-wide, bursaries and financial support from the government’s National Scholarship Programme, worth £150 million a year, and matched funding from universities will reduce the average cost to the student to £7,793, according to the access watchdog.
Sally Hunt, general secretary of University and College Union, said the figures were an embarrassment for the government.
“Ministers made much of the fact that fees of over £6,000 would be the exception. Quite clearly that is not the case,” she said.
“The rubber-stamping of higher fees will entrench our position as the most expensive place to study a public degree in the world.”
Offa published the figures after working with universities over a period of several months on plans to improve access among students from poorer backgrounds.
Institutions wishing to charge undergraduate fees of more than £6,000 a year from 2012 were told to submit new access agreements to Offa.
Sir Graeme Davies, director of Offa, said pressure from the watchdog had resulted in 55 of 123 universities investing an additional £21 million to their access packages.
“It has been a very vigorous process,” he said. “All the providers took terribly seriously their responsibilities to improve access.
“We asked institutions to be ambitious and set stretching targets. In some cases, we felt their goals were a bit soft and needed to be hardened up.”
But he admitted that no universities had lowered their fees in response to the process.
Gareth Thomas, Labour shadow universities minister, said: “Not one university that increased fees to £9,000 has been told to lower their fees and not one access agreement has been rejected...Students and their families will feel let down by the government's cavalier treatment of their hopes and dreams for access to England's universities.”
Under the plans, universities will devote a portion of their tuition fee income over £6,000 towards initiatives to increase access for students from disadvantaged backgrounds.
Universities from the Russell Group will hand over about 30 per cent of this income – about £1,000 a year – to fund fee waivers and bursaries for poorer students.
For instance, by 2015, the University of Cambridge will donate 32 per cent of fee income above £6,000, University of Bristol 35 per cent and University of Birmingham 31 per cent. The University of Oxford will give 51 per cent.
But Martin Lewis, head of the Independent Taskforce on Student Finance Information, said fee waivers should be “irrelevant” to students because many would never pay off their debts in full.
He said a lot of graduates on starting salaries of £30,000 would not fully repay debts incurred from a degree with fees of £6,000 before the 30 year cut off.
As such, attending a university with higher fees would not cost them more.
Mr Lewis said: “It would be a tragedy if young people were put off going to university because of misplaced concerns about the true cost. Our analysis has revealed that only the top graduate earners will pay back their fees in full.”
Vince Cable, the Business Secretary, said: “The government tasked Offa with setting more demanding tests than in previous years. We are satisfied that universities and colleges are showing their determination to improve. Indeed, by 2015, we expect the sector's investment in access to be more than £600 million.”
Nearly all Russell Group universities will charge £9,000 for all courses. But Wendy Piatt, the group’s director general, said she was proud of the universities’ access plans.
“By 2015-16, Russell Group universities will be spending collectively £28.8 million on outreach activities and £153.7 million on fee waivers, bursaries and scholarships for students,” she said.
“Russell Group institutions will be investing 32.3 per cent of their fee income above £6,000 in these measures to widen access to poorer students – significantly more than many other universities.”
However, Les Ebdon, chair of the Million+ group of new universities and vice-chancellor of the University of Bedfordshire, said the average fee level sector wide was “far higher” than the government had intended.
“This reflects the impact of the coalition government’s policy of cutting public investment in university teaching by 80 per cent,” he said.
The university with the lowest average fee is London Metropolitan University, which will charge an average of £6,589 for its degree courses in 2012.