A crime scene was established at the store in Hadfield on West Street after the Wednesday morning fire was deemed suspicious.
An arson chemist is expected to attend the scene.
Detectives from the specialised Lunar Taskforce will investigate if the fire is linked to a series of arson attacks on tobacco stores dating back to March.
More than 27 Victorian businesses have been firebombed over the past seven months as part of a gangland war over illegal profits, police said.
The conflict centres on both the physical placement of illicit tobacco in stores and demands to pay a weekly "tax" to crime syndicates in order to operate.
Police believe Middle Eastern organised crime groups and outlaw motorcycle gangs are recruiting youths and low-level criminals to carry out the offending.
The Victorian government is considering recommendations by former commissioner for better regulation Anna Cronin to tighten up rules in the tobacco trade.
The government was using her report to inform work that would strengthen the Tobacco Act and curb the sale of illicit tobacco, a government spokeswoman said.
"There have been a number of significant changes since the report was provided, including the Commonwealth government's ban on the importation of vaping products without a prescription," the spokeswoman said.
"We will continue to work closely with Victoria Police and other relevant agencies on these issues and the recommendations and provide a response early next year."
Police are also investigating whether the broad-daylight shooting death of a 27-year-old man in a Craigieburn shopping centre car park on October 7 is connected to the tobacco feud.
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