The reduction in the incentive payments comes as teacher training courses report reduced enrolments at primary level and in most secondary subjects.
Jim Knight, schools minister, said primary school rolls were falling, so bursaries would be cut from pound;6,000 to pound;4,000 next year. At secondary level, English, dance and drama had been priority subjects, but there was now an over-supply of qualified teachers, so bursaries in those subjects would be cut from pound;9,000 to pound;6,000.
"This is not, of course, to say that we have all the teachers we need," Mr Knight said. "There are still shortages in maths and science, in London and in representation by ethnic minorities."
So far this year, PGCE enrolments for primary training have dropped about 5 per cent compared with June 2006, and there are reductions in secondary subjects such as English (8 per cent) and drama (4 per cent).
But a Department for Education and Skills spokesman said demand for those courses was healthy, saying it was time to "reduce unnecessary pressure on the public purse".
The worst enrolment drops are in geography (22 per cent), IT (25 per cent) and business studies (21 per cent), according to the latest figures from the Graduate Teacher Training Registry.
The geography numbers reflect fears that the subject may be suffering from an outdated curriculum, while drops in IT and business studies are thought to be caused by a strong economy offering alternative careers. In shortage science subjects, the fall in applications is slowing, but chemistry was still down 3 per cent. Physics was up, but only by 0.3 per cent.
The Training and Development Agency for Schools will continue to pay Pounds 9,000 bursaries for secondary shortage subjects of maths, science, modern languages, RE, design and technology, IT and music. In all other subjects, the agency has reduced the places it is funding. A spokesman said funds needed to be targeted to attract trainees to key shortage subjects.
"There is now strong recruitment to most subjects and healthy competition for jobs in schools," he said. "The overall number of teachers we need will also begin to fall, along with pupil numbers, for the next few years."
Overall, the popularity of the PGCE as a route into teaching dropped 6 per cent, with primary courses accounting for the biggest fall. The only major subjects to significantly increased enrolments are music, RE and citizenship.
Professor John Howson, from analysts Education Data Surveys, said: "The first round of students to pay top-up fees will be graduating during the 2008-2011 pay deal, which has been set at a below-inflation 2 per cent.
With mounting debts, why are they going to do a PGCE year?"
More students could decide on a school-based route into teaching, or opt for a different career.
There are not yet enough enrolments to fill the funded places in key shortage subjects, theJpreliminary figures show. Dr James Rogers, of the Universities Council for the Education of Teachers, said it would be a challengeJtoJfill those places, and bursaries remained important.