Lindsay Handren says the province's universities are running into deficit, a clear signal that university operating grants are falling short.
The student group said Wednesday that recently-posted budget documents revealed the University of New Brunswick, Mount Allison University and the University of Moncton are operating with deficits ranging from $400,000 to $3.6 million.
Handren said New Brunswick ranks eighth in Canada terms of public funding to universities, ahead of only Ontario and Nova Scotia.
"You're going to lose resources and you're going to lose teaching staff," she said. "Universities that can't raise tuition are raising student fees or residence fees."
New Brunswick's Liberal government has frozen tuition and operating grants as it tries to deal with its own deficit — projected at $477 million this year.
Francine Landry, the minister of post-secondary education, training and labour, issued a statement Wednesday saying that universities and colleges understand the challenges New Brunswick is facing.
"We will continue to work as partners in the best interest of students and with the goal of developing a qualified workforce for the province," she said.
Landry said operating assistance to universities will be maintained this year at $217.4 million.
The previous Progressive Conservative government had promised three per cent annual tuition hikes and a two per cent annual increase in the operating grants.
Eddy Campbell, president of UNB, said costs continue to rise while his university's largest revenue sources have been frozen.
He said the $3.6 million shortfall is the first net deficit budget UNB has presented since 2010.
"We will pursue increased revenues through new investments in a number of initiatives, including student recruitment and retention strategies," Campbell said in a statement.
Annie Sherry, chairwoman of the board for the Student Alliance, said it's not sustainable in the long-term to have students cover the rising costs of post-secondary education on their own.
"We recognize the fiscal challenges the province faces. But we also believe that the education and retention of New Brunswick's youth will be critical to its recovery," Sherry said.
She said government needs to support universities by way of increased operating grants.