Flynn says provincial mediators working with the University of Toronto and York University are optimistic deals can be negotiated with TA's and contract staff represented by the Canadian Union of Public Employees.
York cancelled classes on Tuesday for 40,000 students after its 3,700 teaching assistants set up picket lines, but says libraries, residences, computer labs, cafeterias and athletic facilities will remain open.
About 6,000 teaching assistants at the University of Toronto walked off the job Monday after rejecting a contract offer, but most classes at the U-of-T have not been cancelled.
CUPE says about two-thirds of undergraduate courses at the universities are taught by non-tenured staff who are paid about $15,000 a year.
The union wants annual contracts replaced with three-year agreements to ensure job security for teaching assistants.
Flynn said he doesn't think there's any major issues blocking agreements at either university.
"I'm not hearing they're entrenched at all at this point," he said. "Negotiations are obviously tough by nature, but we're hoping that if can get cooler heads to prevail that all the issues can be sorted out at the table."
Colleges and Universities Minister Reza Moridi said the government's top priority in the strikes is looking out for the students' well being.
"We urge the universities and the unions to come to an agreement as soon as possible, keeping the best interests of their students in mind," he said.
Moridi rejected arguments put forth by the universities and CUPE that chronic government underfunding of Ontario's post-secondary sector is behind the labour disputes.
"It's not true," insisted Moridi. "We have increased the funding for universities by 86 per cent, and per student funding has been increased by 29 per cent, so we have done quite a lot for our universities since we came into office in 2003."
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