The students had refused to leave the dorms after the university decided to close some facilities, the Sudan Tribune reported.
Police and security forces also were clashing Tuesday with university students as they tried to march in a peaceful protest to the office of the university's director. The protest came a day after the university's director, Sidiq Haiati, denied the decision to close the university is politically motivated.
The university has been the site of widespread demonstrations since mid-June over worsening economic conditions.
Haiati said the university decided to close during the Islamic holy month of Ramadan because many faculty members have finished their terms.
He denied reports he had resigned after being ordered to close the university by Mohammed Atta, the director-general of the Sudanese National Intelligence and Security Services.