Officers said the goods found are believed to be worth an estimated £1.6 million in lost duty and taxes.
The seizure led police to uncover a tobacco factory in Hamilton, South Lanarkshire, which was dismantled with the seizure of two industrial mixing machines, a tobacco shredding machine, packaging and 45kg of tobacco.
In an operation supported by Police Scotland, three men from Airdrie, North Lanarkshire, aged between 25 and 34 were arrested and charged with Excise Duty fraud and money laundering offences.
Some £20,000 cash was also seized from one of the properties.
Officers aid a report would be submitted to the Procurator Fiscal in due course.
The three men have been released pending further investigation.
Joe Hendry, Assistant Director, Fraud Investigation Service, HMRC, said: “This is another example of the combined powers our partners at the Scottish Crime Campus and Serious Organised Crime Taskforce have to disrupt, detect and deter the illicit trade of tobacco and other forms of criminality.
“Tackling criminal trade is at the heart of our strategy to clampdown on the illicit tobacco market, which costs the UK around £1.9 billion a year. This is theft from the taxpayer and undermines legitimate traders.
“We encourage anyone with information about the illegal sale of cigarettes to report it to HMRC online at gov.uk or call our Fraud Hotline on 0800 788 887.”