Niger's only university has been closed temporarily after running battles between students and security forces.
These have not been the first protests over education
More than 40 people were injured and 300 arrested in clashes as students demonstrated about the non-payment of their grants.
Police fired tear gas at the students to prevent them from crossing a bridge in the centre of the capital, Niamey.
Only some 200 of the 7,000 students remained on campus after Thursday's midnight deadline to vacate.
Last month, student leaders declared a state of permanent protest against what they described as the deterioration of their working and living conditions.
The BBC's Idy Baraou in Niamey says the government accuses the students of Abdou Moumouni Dioffo University of vandalism after they set alight about 10 cars and set ablaze tyres.
Ousmane Bounou from the ministry of education said their fee demands were uncalled for.
"They are telling lies, everything we do, we are doing in collaboration with them," he told the BBC's Network Africa programme.
But students say they have not received fees under a scholarship programme since January.
"We're claiming for six months of scholarships and we're claiming for our health and living conditions... about the rooms, restaurant and our buses," said Zakaria Hakiboun, a striking student.