Two policemen were among the dead during a riot which broke out in the port city of Dakhla on Sunday.
Morocco's interior minister has ordered an inquiry into the violence.
One report said the violence flared after Sahrawi activists, who are seeking independence for Western Sahara, became involved.
At least 20 were injured during the riot and some local businesses were burnt, reports said.
One witness told the AFP news agency that clashes had broken out after "a group of supporters assaulted a Sahrawi".
Morocco annexed the former Spanish territory in 1975. Since then, the area has been the subject of a dispute between Morocco's government and an independence movement, backed by neighbouring Algeria.
Seven people were killed in violence that erupted after a football match in Morocco's disputed Western Sahara region, the state news agency reports.