A last-minute concession by the Government over its higher education Bill will ensure that teacher recruitment is monitored when university top-up fees are introduced.

Unions have warned that newly-qualified teachers will be among the worst hit by annual fees of up to pound;3,000 from 2006, because they will have to start repaying them the moment they begin work.

Mary Bousted, general secretary of the Association of Teachers and Lecturers, said that numbers on postgraduate teacher training courses would be damaged but the impact would be even worse on undergraduate courses.

“This will further damage teacher recruitment because these courses play a vital part in widening access, particularly for mature entrants, returners, and students from ethnic minorities,” she said.

Ministers made the concession shortly before they won the five-vote victory in the Commons on the higher education Bill this week. The Bill scraps up-front tuition fees but allows universities to charge students up to pound;3,000 per year, repaid after graduation once they earn more than pound;15,000 a year.

The decision that the Department for Education and Skills must report on the effect of fees on teachers and other public-sector workers was welcomed by former Labour chief whip Nick Brown.

He said it was a key reason he made a last-minute U-turn and voted for the Government instead of with the 72 rebels. Other concessions include plans for a report on the impact of fees on students from families earning pound;15,000 to pound;21,000.

But Doug McAvoy, general secretary of the National Union of Teachers, said the Bill would still lead to an extension of the “market place philosophy” to secondary and primary education. “Once the principle of variable payment for more or better education is established ... then it is right for us to fear the extension of that principle elsewhere in the education service.

“This leads me to fear that parents will be asked to fund better class sizes and qualified teachers rather than the use of unqualified person to teach children,” he said.

The DfES insisted this would not happen and Mr McAvoy’s fears do not appear to be shared by other teaching unions.

Only one Conservative sided with the Government. Robert Jackson, MP for Wantage, a member of the Commons education select committee and former Tory higher education minister.

He told MPs that the Government’s plan to create an access watchdog was important because demand for university places among the poor was too low.

Three of the other 10 members of the education select committee - Labour MPs Valerie Davey, Jeff Ennis and Helen Jones - abstained from the vote.