Emergency services were called to reports of a fire at the mosque on Bostock Avenue in Manifold Heights about 2.10am.
Seven crews responded to the call and it took them almost an hour to bring the fire under control.
Inspector Graham Banks said the incident is very similar to other recent arson attacks in the area.
“It is one of a series of fires against places of worship in the Geelong area,” he said.
Insp. Banks confirmed this is the fifth targeted attack on a religious building since October 2015, but said it does not look to be an attack on Islam.
“We are not at stage comfortable in saying that this is an attack on the people of the Muslim faith,” he said, suggesting that the arsonists may have mistook the converted mosque for a Christian church.
Firefighters were forced to fight the enormous blaze from outside the building due to concerns it may collapse.
Due to their efforts, there was no damage to any surrounding homes and no one was injured.
The mosque was home to the Islamic Society of Geelong which, according to its website, represents more than 8000 Muslim families.
The venue provided those families with a place of worship as well as providing the community with a space for “meetings, seminars, classes and community gatherings”.
Police have deemed the fire as suspicious, but are treating the incident as a random act.
An arson chemist and detectives will be on scene today.