The university announced on Tuesday it was relocating undergraduate healthcare degrees to the campus in Londonderry.
Diane Dodds said that was a “step forward” for the north west campus but warned of concerns about Coleraine.
Mayor Brian Tierney said: “We should be questioning is the minister committed to New Decade, New Approach?”
Dianne Dodd’s DUP colleague East Derry MP Gregory Campbell said there was “no doubt” the minister was committed to the deal.
On January 11, 2020, the main political parties in Northern Ireland returned to power-sharing after three years of deadlock after agreeing to the New Decade, New Approach Deal.
An agreement in the deal was to bring 10,000 student places to Derry’s university campus.
The decision to move the School of Health Sciences to Magee will bring more than 800 undergraduate students to study at the campus from 2022.
UU’s School of Health Sciences courses include diagnostic radiography, occupational therapy, radiotherapy and oncology, physiotherapy, podiatry and speech and language therapy.
Speaking to BBC Radio Foyle, Mayor Tierney said: “I was disappointed to read the statement from the minister [Dianne Dodds] yesterday.
“For me, there is a commitment to New Decade, New Approach to bring 10,000 students to Magee.
“I think, as a city, we should be questioning is the minister committed to New Decade, New Approach?
“Is she committed to the expansion of Magee and improving facilities across the city and district?”
Speaking on Tuesday, Dianne Dodds said: “Many in the Coleraine area, who had expected these courses to be moved to their local campus, will now be left disappointed,” she said.
The DUP minister said she understood UU’s aspiration is to be “a multi-campus institution with a presence across Northern Ireland”.
“Therefore, it is important that the university now demonstrates that Coleraine maintains a central place in its plans by moving some additional courses there,” she said.
Mrs Dodds said she is to meet UU’s Vice Chancellor Paul Bartholomew and press him “on his plans for balance across all of the university’s campuses”.
Dianne Dodd’s party colleague Gregory Campbell rejected any suggestion the minister was not committed to the New Decade, New Approach deal.
The East Derry MP said the mayor’s comment’s displays the “misunderstanding between the likes of people representing the north coast” and those representing Derry.
“There is a feeling in Coleraine that when Magee benefits, Coleraine loses and there is in Londonderry a feeling that when Coleraine benefits, Magee loses.
“This shouldn’t be a zero sum game – that is what the minister was drawing attention to,” Mr Campbell said.
UU first outlined the plans, which have now been given the green light following a period of public consultation, to move its healthcare courses to Magee in February 2020.
A UU spokeswoman said it was committed to “achieving a better campus balance”.
She added: “Coleraine campus is a thriving and distinguished centre of academic excellence across both research and teaching in diverse disciplines including education, journalism, geography, biomedical science and pharmacy.
“Over recent years the university has invested £27m in facilities on Coleraine Campus, including a £5.1m sports complex for staff, students and the local community.”
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