Student leaders have claimed that top-up fees for England have cut the choices of Scottish students.
Mandy Telford has pledged to battle the reforms
The National Union of Students said the higher fees would stop students travelling south of the border.
The legislation for variable tuition fees in England went through the Commons on Tuesday, despite a majority of English MPs voting against it.
Scots Labour MPs who backed the government have been accused of ignoring the interests of constituents.
NUS president Mandy Telford said the union was determined to stand firm to beat variable fees, which she claimed would have a significant impact north of the border.
"Whether you think students should pay or not, the market is the worst impact of this bill," she said.
"All of a sudden education for students in Scotland will become so much cheaper. Scottish students will not want to leave Scotland."
And would it be cheaper for students in England to study in Scotland - and where would the money for Scottish universities come from?
Meanwhile, Deputy First Minister Jim Wallace has hinted that there could be more cash for Scotland's universities.
But he gave no indication of where the funds would come from, although he laid down a marker that his party would not stand for top-up fees being introduced through the back door by hiking up the "graduate endowment".
Although First Minister Jack McConnell has ruled out top-up fees for as long as he remains first minister, there have been suspicions that the endowment - the £2,000 payment made by Scottish graduates into a fund to provide bursaries for the less well-off - could be raised over time to generate cash for universities.
Scottish universities have called for more funds
But Mr Wallace, the Scottish Liberal Democrat leader, told BBC Radio's Good Morning Scotland that the endowment was ringfenced by law, could only be used for student support, and could not be used for back-door fees.
"It was put there quite deliberately, so that we could not be accused of it being back-door tuition fees, in spite of what some of our opponents have said.
"There certainly would not be a majority, I believe, in parliament for changing it and I don't think we want to give away what's a hard-won provision."
He said the issues would be examined in the upcoming spending review, coupled with a study of higher education funding due to report shortly.
"As Jack McConnell said and as I have said, we want to maintain Scotland's competitive edge and that will undoubtedly require additional resources," said Mr Wallace.
Scottish universities have argued they will need at least £100m to counter the staff and research brain-drain likely to be caused by English top-up fees.
Mr Wallace declined to give an indication of how much the executive would provide.
After Wednesday's vote, which backed top-up fees by 316 votes to 311, Tory shadow education secretary Tim Yeo said: "It is completely wrong that a bill which imposes higher charges on students attending the English universities should only be carried by this House using the votes of Scottish MPs, when the students attending universities in the constituencies of those Scottish MPs do no have to pay those higher charges."
A total of 46 Scottish Labour MPs voted with the government, and five voted against - Michael Connarty, Tam Dalyell, Ian Davidson, Iain Luke and Gavin Strang.
Three more Scots MPs abstained - Robin Cook and Malcolm Savidge, and Jimmy Wray who has been ill and was absent.