Warrants were executed at 16 shops in Ballarat, Shepparton, Yarrawonga and Seymour on Thursday.
Almost 40,000 vapes with a street value of more than $1.1 million were taken.
More than 610,000 cigarettes worth $760,000, 153kg of loose tobacco worth $280,000, and $16,000 in cash was also seized.
The warrants were part of the Taskforce Lunar investigation into organised crime syndicates in the illicit tobacco trade.
There have been more than 30 serious incidents and firebombings linked to a conflict between rival groups since March.
Victoria Police say the dispute is believed to include members of Middle Eastern organised crime groups and outlaw motorcycle gangs that use youths, street gangs and low-level criminals to carry out offending.
Last week, six people were arrested and more than 30 retail outlets searched.
The total value of goods seized over the past fortnight is more than six million dollars.
Victoria Police Detective Superintendent Jason Kelly said there was an incorrect perception it was easier to hide out from law enforcement in country areas.
"People might mistakenly believe they are safe from being targeted and out of constant law enforcement attention," he said.
"That couldn't be further from the truth."
Authorities are calling on anyone with information about the illicit tobacco trade or serious incidents to come forward, particularly store owners and staff.
Det Supt Kelly has previously said a large portion of Victoria's 800 tobacco shops have been infiltrated by criminals and lives were at risk.
The Victorian government is considering recommendations by former better regulation commissioner Anna Cronin to tighten up rules in the tobacco trade.
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