A total of 435 have been expelled or suspended since the start of the protests, the national council of student unions said on Tuesday in reports from Farsi media outlets.
It said a “significant number” of students had been suspended and expelled in an “illegal process”.
Students have played an active role in the protests and are at the centre of Iran's increasingly hardline policies, with universities recently instructed to deny services to female students who break Tehran's compulsory hijab laws.
University campuses turned into battlegrounds between security forces and students, who were tear-gassed and beaten as they staged sit-ins across the country following the death of Ms Amini in morality police custody.
Classes were moved online at Iran's top scientific university following protests at Sharif University of Technology. Hundreds of students were detained and imprisoned. Some were held at Tehran's notorious Evin prison — dubbed “Evin University” by some due to its large population of highly-educated inmates.
Human rights groups reported the suspension of Mohammed Ali Habibi from Tehran University's medical school for “publishing material in support of the protests”.
Graphic arts student Niloufar Mirzaei has also been suspended for two semesters from Alzahra university, a women's college in Tehran.
She was arrested during the protests in November and released in February.
The university issued the suspension “in absentia” while she was imprisoned, the US-based Human Rights Activists news agency reported. It said she had been banned from university dormitories for the rest of her studies.
'Hijab committees' in place
Authorities have already ordered universities to suspend services for female students who do not wear the hijab — a legal requirement under Iranian law.
Female students in the city of Yazd have been told to report to a hijab committee in the case of “non-observance,” Radio Farda reported this week.
Students who do not do so within 24 hours will be deprived of “all services,” read a text to students. The services include food and dormitory access.
Several medical students in Tabriz have also been reportedly suspended for protesting over suspected poison attacks at girls' schools across the country.
Thousands of pupils — mainly girls — have been affected by the attacks, which have left many short of breath and others in a critical condition in hospital.
Sixty students were taken to hospital in Kermanshah on Tuesday, human rights groups said. It is only one of several recent incidents which have worsened concerns over Tehran's growing crackdown on young people.