Police said between 15 and 20 people were in the mosque in the Swedish town of Eskilstuna when the fire broke out at around noon on Thursday, Deutsche Welle reported.
Of the five injured, two were treated for smoke inhalation, two suffered lacerations and one a foot injury.
Police said they were treating the fire, which forced the evacuation of several nearby apartments, as an arson.
"A witness saw somebody throw an object through the window of the building, which serves as a mosque, after which a violent fire began," police spokesman Lars Franzell said.
There was no word on the possible identity of the suspect and there was no immediate claim of responsibility. The mosque is used primarily by Somali Muslims in the town, according to the KNA news agency. Eskilstuna is located about 90 kilometers (56 miles) west of Stockholm.