The more hardline ASSE group says it will skip the upcoming summit because the Parti Quebecois government has refused to consider the option of free university tuition.
Instead, group spokesman Jeremie Bedard-Wien says he's calling for a large popular and student demonstration during the summit on Feb. 26.
Marois says she regrets the group's decision and points out the event will discuss a variety of subjects, not just tuition fees.
She won't rule out a tuition increase tied to inflation.
Many student groups are pushing for a freeze on tuition rates.
Marois says the quality of instruction and research is also on the agenda.
"They are depriving themselves of a place to speak," Marois said on the way into a caucus meeting. "It's a shame but that is their choice and I respect it."
Bedard-Wein says the government has reneged on promises made during last fall's election to hold a real dialogue on the issue.
"This summit doesn't resemble the thorough reflection on the future of our universities, on the fundamental mission of the education system," he said. "It's just to legitimize decisions taken behind closed doors such as, for example, the indexation of tuition fees that no one at the summit table wants."
He said his group "has no other choice" than to walk away.
Huge protests erupted last spring over the former Liberal government's planned increases, with tens of thousands of students taking to the streets.
Marois scrapped the increases after the PQ took power in September.
ASSE was part of the most militant student group during the social unrest of last year's so-called Maple Spring.
The federation's website says it represents 70,000 college and university students.
Quebec's two-day summit on post-secondary education is scheduled for Feb. 25 and 26.