One student said his colleagues had been locked out of their halls after failing to pay the fees demanded by the administration.
"They locked the doors but all our clothes and belongings were still inside and we have nowhere else to sleep," said 21-year-old student Badr al-Din from White Nile state, who asked that his full name not be published.
"So the students got angry and set fire to the offices of the student support fund," he said on Saturday.
Muhammad, a student who also declined to give his family name, said between 50 and 100 armed police had fired tear gas into the crowd and beaten students with sticks to disperse the demonstration.
Police at the scene said no one was hurt in the disturbance, which began at about 5pm (1400 GMT).