The tower block that housed the prayer room had to be evacuated as huge clouds of smoke wreathed the building.
Police had first stated the fire started when someone threw an object into the room through the window. But this was based on one witness and they have not been able to find any other evidence that there was an attack.
Dogs have searched the wreckage but have not detected any flammable liquids.
Hundreds have demonstrated and politicians have spoken out condemning the alleged attack, which many assumed to have been motivated by anti-Muslim bigotry.
Around 70 people were in the mosque when the fire started, including several children. Five people were taken to hospital.
The Eskiltuna police are still treating the investigation as an arson case.
Vandalism at another Eskilstuna mosque is not seen by police as connected to the fire.