Newport is the fifth Welsh university to set its fees at the maximum ?9,000 per year for some courses.
Students from Wales pay about ?3,400 and the Welsh Government makes up the difference.
Teresa Rees said costs would rise phenomenally. The Welsh Government said its policy was affordable.
Prof Rees, a former pro-vice chancellor of Cardiff University who is on the governing body at Glamorgan University, told BBC Radio Wales it was difficult to see where the money would come from.
University funding is a devolved issue with the Welsh Government paying each student a grant for their costs over ?3,400.
Prof Rees said: "I think the commitment to [people living in Wales] having affordable higher education is absolutely admirable.
Continue reading the main storyBy Ciaran Jenkins, BBC Wales education correspondent
The question is not why Welsh universities would charge fees of ?9,000, but rather why wouldn't they?
Between 50 - 75% of students at each institution are from Wales, meaning the Welsh Government will pay for any fee increases on their behalf.
It's not surprising therefore that universities here are maximising the potential gains from this system.
Three in four students at Glamorgan and Newport will be subsidised by the Welsh Government, so it makes sense for these institutions to charge as much as they possibly can.
It's an entirely different situation to the one facing universities in England, who have to remain attractive to almost their entire student body at three times the price.
"There is a question about the affordability. It's a political choice that's been made but the question is where is that money going to come from."I have a great concern about that because these figures are going to increase year by year. That amount of money is going to increase phenomenally."
A Welsh Government spokesperson said it had made it clear that its tuition fee policy was affordable, sustainable and fully costed to 2016.
"It is important to note that before Welsh Universities can set their tuition fees higher than ?4,000 for academic year 2012/13 their fee plans must be rigorously scrutinised and approved by HEFCW (the Higher Education Funding Council for Wales) to ensure they are meeting our requirements in respect of equality of access to higher education and improving the student experience.
"The minister expects HEFCW to take a robust approach to the assessment of fee plans."
Newport is the latest university to announce it wants to charge the maximum ?9,000 for some courses following Aberystwyth, Cardiff, Bangor and Glamorgan.
It will charge ?8,250 for others and said it had done everything possible to keep its fees down.
'Extremely disappointing'Five more universities in Wales did not declare their fees plans before the HEFCW deadline on Tuesday.
Newport said its decision to propose two rates reflected the difference in the cost of providing courses.
Continue reading the main storyI can't still get my head around paying ?9,000 a year for a course and I think that many people out there can't as well”End Quote Katie Dalton Natinoal Union of Students Vice chancellor Dr Peter Noyes said they had considered "every single option".
"Increasing the cost of study for our future students is not something we do with any relish but is the only option available to us in the situation that we find ourselves in."
Under the terms of the new student finance settlement universities are expected to spend at least 30% of all income over ?4,000 per student on widening access to higher education and improving what they offer students.
Dr Noyes added: "HEFCW have indicated that those institutions better able to meet the Welsh Government's widening participation agenda will be more justified in charging higher fees.
"Newport already has a terrific track record in widening participation. We already recruit large numbers of students from some of the most economically disadvantaged areas of Wales."
Katie Dalton, president of the National Union of Students Wales, said it was "extremely disappointing".
"I can't still get my head around paying ?9,000 a year for a course and I think that many people out there can't as well."
She said it was vital the Welsh Government continued to subsidise the fees.
"They need to make sure that the tuition fee grant does remain in place in future so the Welsh students don't have to pay more."
HEFCW said it would look at every university's plans to increase the fees from 2012 and would announce its decisions on 11 July.
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