A military spokesman claimed the Shield Libya brigade intervened "to prevent student casualties" after a skirmish between Toubou and Zwai tribesmen escalated inside Kufra University.
Local authorities ordered that the university, which is in a Toubou area, shut for two days until order is restored.
A tribal chief called on "the army to secure Kufra, and not a group of civilian revolutionaries who have no military principles".
Kufra, a town of about 40,000 people, is located in a triangle where the borders of Egypt, Chad. and Sudan meet. Fighting last February claimed more than 130 lives and displaced half the population. Last June, 47 people were killed and more than 100 wounded.