At least 12 people may have died in violent clashes with Iran's security forces following President Mahmoud Ahmadinejad's disputed re-election, ­according to reports from the country.

The reported fatalities have come amid a brutal crackdown on students, apparently aimed at quelling a wave of campus rebellions that authorities fear could spill over to the wider population.

A Farsi website, Balatarin, carried an unconfirmed report that seven people had been killed in the southern city of Shiraz following confrontations with riot police at the local university. Five busloads of plainclothes officers had been sent to confront the demonstrators during Sunday's protests, but were said to have been unable to prevent them from being joined by members of the public and marching to one of the city's main squares. It is unclear whether all those said to have died were students.

The Guardian understands that five students may also have died in clashes at Tehran University early on Sunday. The students – named as Fatemeh Barati, Kasra Sharafi, Mobina Ehterami, Kambiz Shoaee and Mohsen Imani – are believed to have been buried today in Behesht-e-Zahra, a famous cemetery in Tehran, reportedly without their families being informed.

Autnews, a student website, claimed that plain clothes officers used firearms against students after forcing their way onto the campus. Students were said to have sought refuge in toilets after police raided halls of residence, where rooms were ransacked and beds set on fire.

Tonight Ali Larijani, the speaker of Iran's parliament, appointed a committee of MPs to investigate the reports.

The reported fatalities appeared to be backed up by one witness, who said a force of around 300 plainclothes and riot police joined basij forces (militia volunteers) to attack the students.

"We had nowhere to hide but the toilets and bathrooms, and they shouted: 'You traitors to the Islamic republic, you bastards, leave the building or we'll shoot you all.' Many students were severely wounded – we could hear injured students groaning and shouting for help," the witness said.

"At 3am they announced on loudspeakers: 'If you evacuate the building we won't harm you. Otherwise, you'll all be injured or killed.' All the students then came out of the building in lines, with their hands on their heads. The police hit them with batons and some started to shout that they had conquered the dorms. Eventually they let us go back to our rooms but at least 10 had been shot, some appeared to have been killed and hundreds were injured."

Another witness, Majidreza Sobhani, 21, a mechanical engineering student, said police smashed locks to force their way into students' rooms. "I can't describe what they did to me and friends. Just go to our dorms and see what our rooms look like," he said.

Violent incidents were reported at Isfahan University, where 60 students were taken into custody following clashes that left halls of residence badly damaged. Some students were said to have been injured after being thrown from upstairs windows.

Protests also took place at Hamedan University and Babol University in Mazandaran province on the Caspian Sea, where demonstrations are said to have spread to four towns after police attacked students.

Riot police surrounded the campus of Tabriz University, which has historically been a hotbed of radical protest.

Anger was apparent too at Amir Kabir University in Tehran, where Ahmadinejad was forced to flee the campus after angry protests more than two years ago. Some 150 lecturers and around 500 students staged a sit-in at the campus mosque, mirroring an action by academics at another Tehran institution, Sharif University, on Sunday.