A police source told AFP that a priest was also injured.
One person was reportedly injured as people scrambled to get inside the church for cover.
The police are seeking witnesses to find the perpetrators.
The act of vandalism took place in broad daylight, in the afternoon.
The damage will cost more than 50,000 euros to repair. An investigating judge is now in charge of the case
The investigation revealed that the group was led by a 59-year-old imam from one of the mosques in Melilla.
The Minister of National Education, Pap Ndiaye, points to the problem of wearing Muslim abai by girls and qamis by boys.
Church attendance among Dutch Catholics has fallen from 80% in the 1950s to only 3%, leading to large numbers of church closusures