Worshippers escaped the religious establishment after the fire broke out on Friday.

According to reports, the synagogue regularly holds overnight prayers.

"Detectives are looking for three offenders believed to be involved," Victoria Police said in a statement.

"They were disturbed by a man attending the synagogue and fled the scene," the statement said.

"Police are working to establish the exact circumstances of the fire and at this stage believe it was a targeted incident," the statement said.

Police said it will conduct additional patrols around the synagogue and surrounding areas.

Prime Minister Anthony Albanese has condemned the incident.

"I unequivocally condemn the attack on a Melbourne synagogue early this morning," the PM said.

"I have zero tolerance for antisemitism," the PM said.

"It has absolutely no place in Australia," the PM said.

The attack took place amid the ongoing conflict between Israel, Hezbollah and Hamas groups.