Suggestions that top-up fees could rise to £15,000-a-year have been rejected as "absurd" by the education secretary.
Lecturers oppose the plans
Charles Clarke made his remarks in a letter to rebel Labour MP Nick Brown.
Opponents of the plans are worried the planned annual cap limiting universities to charging £3,000 per year will eventually be scrapped.
In his letter Mr Clarke wrote: "Any idea that the government is going to sanction fees of £15,000-a-year is quite frankly absurd."
Ministers have been making a concerted effort in recent weeks to allay the fears of opponents of top-up fees and the publication of Mr Clarke's letter is likely to be seen as part of the government's campaign.
The bill - which will be published on Thursday - will allow universities from 2006 to charge variable tuition fees of up to £3,000 a year, repayable when graduates earn £15,000.
Rebels worry the initial £3,000 cap on fees could soon be abandoned, as some university vice-chancellors want to charge more.
Critics also claim the variable rate charged for different courses could cause a "two-tier" system.
In his letter to Mr Brown, the education secretary says the level of bursaries on offer could make some students from lower income backgrounds even better off on the very best courses.
No poorer student will have to increase their debt to get on the top courses and the limit will act as a safeguard, he argued.
Mr Brown has told the BBC he would be prepared to oppose the government on the issue of variable fees in his first vote against the Labour whip since entering Parliament.
He is among the Labour backbenchers and several former ministers who fear the fees may deter students from poorer backgrounds from going to the best institutions.
On Monday, another opponent of the plans, Labour member Peter Bradley, suggested a deal with ministers was "quite possible".
The MP, also parliamentary private secretary to Countryside Minister Alun Michael, said: "I think it is quite possible the government will come forward with a package this week which will address many of my concerns and those of my colleagues.
"I have been very encouraged with the way ministers have engaged with the ideas we have put forward. We will have to wait and see the fruit of their deliberations."
Mr Bradley said he was concerned that poorer universities would be forced to charge the maximum of £3,000 a year because they could not afford not to.
Mr Bradley conceded that tuition fees were inevitable if higher education was to be improved and access widened.
He urged the government to consider putting all the cash raised from top-up fees into a central pot which could be shared among universities.
Conservative leader Michael Howard has also said he has "grave reservations" about tuition fees, but says he is reviewing his party's anti-fees policy.