Members of the Commons education select committee raised the concern when they quizzed Alan Johnson, the minister for higher education, about government plans to allow universities to charge students variable fees of up to pound;3,000 a year.
Helen Jones, Labour MP for Warrington North, said students who planned to become teachers would realise that they would not earn any more by attending a university which charged pound;3,000 instead of pound;1,000.
This meant that many would-be teachers, and other public-sector workers, would avoid applying to the most prestigious or "research-intensive" universities.
However, the claim was dismissed by Mr Johnson, who said that the repayments students will make after graduation will relate to their incomes.
He added: "I think they will go to universities and decide then whether they want to go into the public sector or elswhere. The loan repayment system will give them the confidence to follow the career they want to pursue."
Mr Johnson also dismissed calls for alternatives to top-up fees such as a graduate tax. If the extra billions were not directly linked to universities, staff at the Department for Education and Skills would argue that it could be better spent elsewhere in education, he suggested.
The minister said: "There would be other priorities. The fact that we spend pound;5,500 a year on students in higher education and pound;3,000 a year for those in primary schools is quite perverse."
Speculation was mounting this week that the Prime Minister would tell Labour MPs to "back him or sack him" in an attempt to prevent a Commons defeat in January on the reforms to higher education.