Customs officials say they have seized the biggest ever illegal tobacco shipment uncovered in a single operation.

The Australian Border Force (ABF) said it had seized 71 tonnes of tobacco in three shipments destined for sale in Australia.

Two of the shipments were discovered in Sydney in June, and the third was intercepted before it could leave Indonesia.

Border Protection Minister Peter Dutton announced an ABF strike force would now be formed to target illegal tobacco shipments.

He said the tobacco would have been worth $40 million on the black market.

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"It would have equated to 67,000 packets of cigarettes per week over a 12 month period, which means for teenage kids, for Australians otherwise, this tobacco would end up in their hands," he said.

"Also, it means that Australian taxpayers would have been dudded to the tune of about $27 million."

The ABF said it had identified the syndicate behind the shipments.

"The operation is still ongoing. Investigations are continuing," ABF commissioner Roman Quaedvlieg said.

"We are now at a point in the operation where we are able to publicly announce the seizure. We have a very strong idea who has brought it in."

The seizure follows yesterday's haul of almost six million allegedly illegal cigarettes after raids of storage centres and homes in Melbourne.

Nearly 10 tonnes of tobacco products were discovered to have been smuggled into Australia from the United Arab Emirates in June, according to the ABF.

Last month, police charged a dozen people accused of being involved in a multi-million-dollar cigarette smuggling operation in Sydney.

The tobacco was discovered in two shipments in Sydney and one in Indonesia. ( ABC News: Siobhan Fogarty )

Police said that operation involved corrupt waterfront officials, and the group helped smuggle large quantities of illegal cigarettes and tobacco into Australia, including a shipment of nine million Manchester branded cigarettes from the United Arab Emirates.

The cigarettes had a black market value of about $5.4 million.

Mr Dutton said a high degree of organisation was needed for such large shipments.

"There are clear links to organised crime and we know that groups smuggling illicit tobacco into Australia are also involved in other illegal activities such as narcotics," he said.

"The ABF is determined to disrupt their activities and the new ABF strike team will focus on the organised crime syndicates behind shipments like this and collect intelligence on their operations."

Mr Dutton said co-operation between ABF and Indonesian Customs had ensured the operation's success.

"Their long, constructive links over many years are crucial in disrupting the operations of transnational criminal organisations dealing in illicit drugs and tobacco," he said.

"I welcome the efforts of our Indonesian friends in achieving this outcome."

The information gathered will be shared with existing organised crime task forces and other agencies.