Students at the Syiah Kuala University, the most prestigious college in the badly-hit western province, demanded that fees be waived and called for the resignation of a chancellor who had issued the order.
The noisy demonstration was held outside a center where a seminar on post-tsunami Aceh was being held. Several armed policemen at the scene made no attempt to intervene or to disperse the students.
"We call on all students not to pay the study fees... the people of Aceh and students of Syiah Kuala University are still recovering from the natural disaster," the protestors said in a statement.
They urged the university to ensure that temporary housing for students and teachers, who lost their homes in the tidal waves, were ready by March. The students vowed to continue their protests until their demands were met.
The state university, near the Malacca Strait coast, was swamped by the waves that engulfed at least half the provincial capital Banda Aceh on December 26 as mid-term examinations were underway.
Officials say the university lost 110 staff and 1,000 of its 23,000 students in the catastrophe that killed an estimated quarter of a million Indonesians.
The campus grounds have been filled with tent camps, both for families displaced by the tsunamis and for Red Cross volunteers. Some displaced people were also sleeping in classrooms.