The biggest cocaine bust in Australian history can be traced back to a burnt-out truck on a remote coastline.

Australian Federal Police uncovered 2.7 tonnes of cocaine buried in plastic tubs in makeshift bunkers underneath shipping containers after executing a search warrant at a semi-rural property in outer western Sydney on June 19.

It is the biggest Australian drug bust in nearly 20 years, and second only to the seizure of 4.5 tonnes of MDMA in Melbourne in 2007.

Two men allegedly tried to run from police after officers discovered the drugs, with an estimated value of $816 million - equivalent to three million street-level deals - buried under the false flooring.

The men, aged 21 and 25, were arrested after an investigation by the AFP, alongside Australian Border Force and state police as part of Operation Minjiang.

They were each charged with possessing a commercial quantity of an illegal drug, which carries a maximum sentence of life imprisonment.

The men were refused bail on Saturday and are expected to face Penrith Local Court on August 13.

It is understood the men were foot soldiers in a massive operation involving the Coconut Cartel syndicate, which includes former members of a prominent Sydney crime family.

The investigation was triggered three weeks ago by the discovery of 40kg of cocaine floating in the water, close to a burnt-out truck at Midge Point near Mackay on the central Queensland coast on May 30.

A series of search warrants across north and southeast Queensland, along with one in Sydney, resulted in six people being charged with varying offences including possessing illicit drugs and dealing with proceeds of crime.

On Thursday, the Queensland Joint Organised Crime Taskforce announced they had seized 178kg of cocaine and 142kg of meth - bringing the total of drugs seized to over three tonnes - during a three-week investigation.

But that announcement was dwarfed by Friday's discovery.

The alleged mothership used to import the haul of drugs, MV Wealth, has been detained by authorities in the Solomon Islands for further investigation.

The vessel is registered in Belize, Central America, but the origin of the drugs - which could have been loaded anywhere from South America to northeast Asia - is still under investigation.

'This alleged plot to distribute nearly three tonnes of cocaine ... demonstrates how highly organised and determined these criminal networks are,' AFP Commander Stephen Jay said.

Mr Jay hinted that the disruption of the plot could mean more violence between warring gangs, which he said was 'baked in' to their operations.

'Someone's lost a lot of money,' he told reporters in Brisbane on Monday.

'Violence is baked into the organised crime networks intrinsically [but] from a policing perspective, NSW police, the AFP, Queensland police, law enforcement is ready to respond.

'There'll be some soul-searching, no doubt, about losing Australia's largest quantity of cocaine.'

Queensland Police Acting Chief Superintendent Troy Pukallus said he was proud of his officers' tenacity in disrupting a massive organised crime syndicate.

'What began with the actions of Mackay police ... evolved into a sophisticated, multi-agency investigation targeting an organised criminal network,' he said.