In a series of decisions on Tuesday, Sudan's military leader General Abdel Fattah al-Burhan dismissed the boards and appointed new heads for some 30 national universities.
Burhan is tightening his grip after taking power in a coup in October, reversing appointments made by civilian leadership during a two-year power-sharing period.
In a statement, the head of the board of governors for the University of Khartoum, Sudan's most prominent university, described Burhan's decisions as illegal and encroaching on powers held by the prime minister. Professors at Sudan University, one of the largest, said they would begin an open-ended strike in protest.
Military leaders have yet to appoint a prime minister since the resignation of Abdalla Hamdok in January following a brief return to office.
Universities have been a hotbed for student protests, and university presidents had been involved in mediation attempts between the military and civilian groups.