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Senior student leader Abdollah Momeni said up to 2,000 students had gathered for the protest over the expulsion of some students and the way authorities had been handling critics.He added 20 had been seized by Islamic vigilantes who broke into the dormitories.
"The main reason for the objections in recent days goes back to the limitations imposed on universities and political students after the new government came to power," Momeni said.
Religious conservative Ahmadinejad was inaugurated in August.
"Some active students have been expelled and some students face mass summons before disciplinary committees. We are also objecting to recent dealings with critical professors such as Ramin Jahanbegloo," he added.
Iran earlier this month said it had arrested philosopher Jahanbegloo on charges of espionage. He specialized in liberal political philosophy and worked extensively on developing understanding between Iran and the West.