Clashes erupted at Assiut University in Upper Egypt on Tuesday when protesting students tried to march off campus and security forces fired teargas to stop them, Al-Ahram's Arabic website reported.
A new law requires protest organisers to notify police at least three days in advance of any public demonstration larger than ten people; but the legislation does not apply to protest on university campuses.
According to Al-Ahram's Arabic website, protesters threw stones at the security personnel deployed in the vicinity. Others placed steel blocks at the university entrance to prevent security forces from entering. As the protest continued, security forces fired teargas into the campus. Students also alleged that police fired birdshot.
The students were calling for the release of a number of Islamist protesters who had been given prison sentences recently, including 21 women and girls in Alexandria who were given 11 year sentences last week for charges related to a protest in support of Mohamed Morsi.
Students at the local branch of Al-Azhar University in Assiut also demonstrated in support of the same demands.
Other universities also saw turmoil as students continued to stage anti-government protests.
At Cairo University, hundreds turned out on Tuesday to protest the death of engineering student Mohamed Reda, killed the Thursday before during clashes between students and police forces.
At Tuesday's protest, many demonstrators held up the four-fingered Rabaa sign, used by supporters of ousted president Mohamed Morsi. The protesters managed to exit campus, and removed steel blocks placed at campus exits by police to prevent the march from leaving university grounds.
Police, who were present at the scene in considerable numbers, did not react to the move off campus.
A hundreds-strong protest against the interim authorities also took place at Ain Shams University in north-east Cairo on Tuesday. Key thoroughfare El-Khalifa El-Mamoun Street was blocked for some time by protesters.
Another group of students demonstrating in support of the military and police scuffled with the opposing protesters, who were chanting anti-military and anti-police slogans. Several students and journalists were reportedly injured.
Nearby, around 200 students blocked Mostafa El-Nahas Street in Cairo's Nasr City district while voicing support for ousted Islamist president Mohamed Morsi.
Protests on university campuses have become common since the beginning of the new academic year in September, with different student groups supporting or opposing the transitional authorities which replaced Morsi.
In November, the cabinet issued a decision allowing police to enter university campuses without prior permission if facilities or students were under threat. Previously, police had been banned from campuses unless specifically invited by university authorities.