Welsh sixth formers who want to become vets will have to pay pound;3,000 top-up tuition fees for courses in England - even though they cannot study in Wales. Their classmates who stay in Wales to study other subjects will only have to pay the current pound;1,200 fee, as the Assembly government is covering the difference.
Officials say EU laws on discrimination mean that stumping up the cash for Welsh students studying in England would also mean non-UK EU residents could apply for the grant.
A cross-party deal made last June means that from 2007-8, Welsh sixth-formers who win places at Welsh universities will not have to pay additional fees on top of the current pound;1,200.
But English and Scottish students studying in Wales will have to pay up to pound;3,000 in variable tuition fees - as will Welsh students studying in England, including courses that are not available in Wales.
Opposition parties and students say that is grossly unfair, and could disadvantage students who may drop out of courses because of debt fears.
Janet Ryder, Plaid Cymru's shadow education minister, told a recent meeting of the Assembly's education, lifelong learning and skills committee: "We are crying out for vets in parts of rural Wales but there are no courses at our universities, and we are not supporting students who want to go to veterinary schools."
Student leaders are also unhappy. A spokesperson for Cardiff university's students' union said: "Students who can't study in Wales are clearly going to be at a financial disadvantage."
But Jane Davidson, minister for education, lifelong learning and skills, said it was not the Assembly government's intention to disadvantage any Welsh student.
She said the government would pay the extra costs for the 10 or so Welsh students studying certain courses - including town planning and medicine - at Oxford or Cambridge universities.
Meanwhile, a leading Welsh vet has called for careers teachers to encourage more boys to go into the profession. It comes as latest figures from the British Veterinary Association (BVA) show 90 per cent of student vets are girls.
Usk-based Bob Stevenson, a former president of the BVA, also called for a Welsh university to provide veterinary science.
He said: "There is a dire shortage of vets around farms in some rural parts of Wales. It has always been thought that one of the universities should offer a course."
Mr Stevenson said girls were often taken on because they demonstrated more drive and work experience than boys.
"Girls can often show they have already been out in the field. They may have been neutering cats in Spain or helping camels in the Sahara.
"But then they are less likely to want to work in quieter places like farms in rural locations later on," he said.
He added: "I hope sixth-formers are not put off applying for veterinary courses, but I know the debt factor is a big thing."