ABUJA, Nigeria—The army killed 347 Shiite Muslims during a December clash, according to a special investigation by a state government in northern Nigeria, underscoring deepening animosity between the Shiites and soldiers in a nation already dealing with Sunni Islamist insurgency Boko Haram.

A report released late Monday by the government of Kaduna state, where the killings occurred, found that the army fired at followers of Shiite cleric Sheik Ibrahim Zakzaky, who is currently detained. Mr. Zakzaky’s followers had taken over...