The letter to Ayatollah Ali Khamenei — signed by 88 professors — was the latest daring challenge to the Iran's clerical leadership.
The letter, posted on the Greenroad Web site, called the attacks a sign of weakness in the ruling system and demanded punishment for those who beat up students. It also urged Khamenei to order arrests over the hard-line crackdown, which intensified after protesters began chanting slogans against the supreme leader.
At least eight people died in clashes between security forces and opposition supporters across Iran late last month, including a nephew of opposition leader Mir Hossein Mousavi.
It was the worst bloodshed since the height of the unrest immediately after disputed June presidential election.
"Nighttime attacks on defenseless student dormitories and daytime assaults on students at university campuses, venues of education and learning, is not a sign of strength. ... Nor is beating up students and their mass imprisonment," the letter read.
The letter referred to attacks by pro-government paramilitary Basij forces on pro-opposition students inside Tehran University campus last month. The attacks were launched after students took to the streets on Dec. 7 on more than a dozen campuses in the biggest anti-government protests in months.
The professors said none of the attackers, who chanted slogans in support of Khamenei while beating students, have been punished. They demanded Khamenei also order that all students arrested in the protests be released.
"Unfortunately, all these (attacks) were carried out under the pretext of protecting Islam" and the position of the supreme leader, the professors also said.
Iranian students were the driving force of the 1979 Islamic Revolution and they led anti-government protests last month that revitalized the opposition movement, even as opposition leaders struggle to dent the power of the ruling establishment.
Tehran University is the country's largest, with 1,480 professors and teachers, according to its Web site.
A fierce government crackdown had all but crushed mass street protests that erupted immediately after June's presidential elections, which the opposition says President Mahmoud Ahmadinejad won by fraud. But the protests regained momentum in December and large turnouts at rallies showed months of arrests and intimidation have failed to stamp out the movement.
The government has accused the West of fomenting Iran's post-election turmoil. Intelligence minister Heidar Moslehi said Monday some of those arrested in protests Dec. 27, when Shiite Muslims in Iran marked the sacred day of Ashoura, were foreign citizens.
"Some of the detainees ... were foreign nationals who were leading a propaganda and a psychological war," said Moslehi, according to state TV. He said the foreigners came to Iran just two days before the Ashoura but did not specify their nationalities.
Moslehi said cameras and equipment belonging to the foreigners was also confiscated.
Iran has been conducting mass trials of opposition figures and activists arrested in the post-election protests. Five defendants have been sentenced to death and 81 had received prison terms ranging from six months up to 15 years.
Authorities said more than 500 protesters following were arrested after the Ashoura protests and that they would be put on trial.
General prosecutor Gholam Hossein Mohseni Ejehei said Monday those trials would be speedy and that some of the detainees could also face the death penalty over rioting against the ruling clerical establishment.