"The southern town of Ain Salah has witnessed riots by a group of youths opposed to shale gas exploration operations in the region," the ministry said in a statement late Sunday.
"Unfortunately, the [riots] left 40 policemen injured, including two in a serious condition," it added, noting that several police buildings had also been torched.
According to the release, calm returned to the town after security forces contained the situation.
Elsewhere, local activist Taqi Abdel-Rahman told The Anadolu Agency earlier that at least 20 people were injured in similar clashes in Tamanrasset – also in southern Algeria.
Protesters in several parts of southern Algeria have held near-daily protests since last December to pressure authorities to halt shale gas drilling in the area.
Estimated at 19.8 billion cubic meters, Algeria is the world's third largest holder of shale gas reserves, preceded by China and Argentina, according to a recent U.S. government report.