The Higher Education Bill would allow English universities to charge up to £3,000-a-year in tuition fees, payable when graduates earn £15,000.

The Welsh Assembly would be allowed to decide whether it would implement the same system. Scotland and Northern Ireland would not be directly affected.

Education Secretary Charles Clarke insists the government will win a crucial Commons vote on 27 January. The government’s optimism has been boosted by a BBC survey which suggests that the proposals will have the backing of at least 27 Scottish MPs, despite the fact that tuition fees would only affect English and Welsh universities.

Mr Howard, speaking on BBC One’s Breakfast with Frost programme, said “We believe it would be quite wrong to have this decision made by the votes of members of Parliament from Scotland, where they do not have top-up fees.”

However, Mr Howard refused to commit his party to sticking by Iain Duncan Smith’s pledge to scrap all fees. “The truth is the universities have a funding problem,” he said. “It has been estimated variously at a £10 or £11 billion shortfall, and neither the government nor ourselves have any proposals to deal with that problem.

Charles Clarke told ITV’s Jonathan Dimbleby programme top-up fees, which would significantly increase student debt, were “not a bad trade-off” for removing “the first two stages of poverty that stop people going to university” – up-front fees and inadequate help with living costs.

Tony Blair is expected to field questions about the controversial policy when he meets Labour backbenchers in private on Monday.