Top-up tuition fees in England have proved controversial
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The bill which allows ministers to raise tuition fees in Scotland for students from south of the border has been strongly criticised.
The move is aimed at stopping "fee refugees" from swamping courses in Scotland when top-up fees take effect in England.
The National Union of Students in Scotland said it marked the thin end of the wedge for fees across the board.
But the Scottish Executive said it was opposed to top-up fees in principle.
A Liberal Democrat amendment on the bill was accepted on Wednesday which will make any extension of top-up fees subject to a 60-day consultation.
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Poorer students will have to choose cheaper courses - that is wrong and doesn't have any place in Scotland
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But Melanie Ward, NUS president in Scotland, said: "We believe that the introduction of the principle of variable fees into Scotland is wrong because, where you pay a different amount for studying a different course, students will inevitably chose what they study and where they study based on price.
"Poorer students will therefore have to choose cheaper courses - that is wrong and doesn't have any place in Scotland.
"We are also worried that these powers are the thin end of the wedge.
'Perceived problem'
"They [ministers] say they want to use it for English medical students first but the legislation doesn't specify that that is all they can use it for.
"We might see a situation arise where it starts with English medical students in Scotland, but then spreads across to dentistry, engineering or to other courses where there is a perceived problem - and to Scottish students eventually.
"We accept that there is a problem with the recruitment and retention of doctors in the NHS in Scotland, but we don't believe that the student funding system is the place to solve that."
Jim Wallace said the executive was trying to protect students
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The fees part of the Further and Higher Education (Scotland) Bill is intended to deal with the the fall-out from annual tuition fees being introduced in England in 2006.
Fees there that are currently a flat rate of £1,150 will vary from nothing up to a maximum of £3,000 depending on the institution.
The executive is concerned that the top-up fees, which could amount to £15,000 for a five-year medical course, could see an influx of English students to Scotland in search of cheaper courses.
Research has shown that about 35% of graduates from Scotland's five medical schools immediately leave Scotland to work, mostly in England, while around half of recruits to Scottish medical faculties are English.
Protection for students
Minister for Lifelong Learning Jim Wallace said the bill would ensure that opportunities for Scottish students were not damaged.
He said: "Having been faced with a situation where there are variable top-up fees in England, we've had to take steps to ensure that it doesn't crowd out students living in Scotland from being able to get places at Scottish universities - in particular with medicine.
"There is no student resident in Scotland that will pay any fee as a result of what has happened."