"I hope that those responsible are caught. The background is not clear, but it is difficult to believe otherwise than that this gross violence was directed against Muslims as a group and Islam as a religion," Swedish Justice Minister Morgan Johansson was cited as saying by the Svenska Dagbladet newspaper.
According to Johansson, the Eskilstuna fire is a "cowardly attack against freedom of religion and individuals."
Meanwhile, Swedish Minister for Home Affairs Anders Ygeman condemned the attack as "disgusting and unacceptable."
"We are not doing enough in terms of protection, whether it's a mosque or any other religious community," he told Svenska Dagbladet, adding that while investigators are yet to determine if the attack was a hate crime, "police has confirmed that it was arson."
On Thursday, five people sustained injuries as a major fire broke out at a mosque in Eskilstuna, some 100 km (60 miles) west of Stockholm.
Shortly after the incident, local police informed that the fire was started by an arsonist and investigators would look into witness reports that suspicious objects were thrown into the building moments before the flames broke out.