Trainee teachers will have to pay up to pound;1,800 towards their tuition fees, leading to fears that many will be put off from joining the profession.
The Office for Fair Access confirmed this week that from 2006 fees will increase to up to pound;3,000 for the one-year post-graduate certificate in education (PGCE).
The Government has promised pound;1,200 for all trainees and up to Pounds 2,700 for the poorest, which will offset some of the costs.
However, the watchdog said that trainee teachers would also be eligible for a series of bursaries.
But universities and recruitment experts have warned that they expect recruitment to fall unless institutions can find larger bursaries to attract would-be students.
The Teacher Training Agency announced last month that it would increase grants for trainees in shortage subjects, such as maths and science, from pound;6,000 to pound;9,000, on top of the pound;5,000 golden hellos they receive when they start their first jobs.
The pound;9,000 grant will also apply to trainees opting for foreign languages, music and religious education, as well as a pound;2,500 golden hello. All other teachers will continue to get the pound;6,000 bursary.
Trainee teachers will have to pay back fees when they graduate and start their first job.
Sir Martin Harris, the director of Offa, said: "We are concerned that the poorest students should not be put off applying to teacher training courses because of the cost.
"Institutions charging the maximum fee will be required to offer the minimum bursary to the poorest students."
James Rogers, executive director of the Universities Council for the Education of Teachers, said: "We welcome the extra-increase investment that fees will bring, but we will keep a particular eye on recruitment next year.
"It is too early to say if fees will have a particular effect.
"But there is concern that primary and non-shortage secondary subjects, which have not received increased bursaries, will suffer."