The 800kg of cocaine with a street value of $320 million was intercepted off the West Australian coast after a multi-agency investigation.
Australian Federal Police Assistant Commissioner Pryce Scanlan said drug syndicates were changing the way they operated.
"Previously, over the years, an order has been placed and the drugs have been sent," Mr Scanlan said in Perth.
"We're seeing a change where the drugs are just put on the water and then the orders are placed."
Australia has one of the world's most lucrative drug markets and some of the highest prevalence of cocaine use in the world, according to United Nations data.
"We pay high prices for our drugs, which makes us attractive to all cartels," Mr Scanlan said.
The discovery of the 800kg haul happened on May 24 after the WA Police Force and Volunteer Marine Rescue WA helped a 10m cabin cruiser in distress near Rottnest Island, about 22km off the coast from Fremantle.
Three men were onboard the cabin cruiser, named No Fixed Address.
Authorities became suspicious after the AFP discovered the cruiser had been bought with cash the day before and hours later was taken out to sea towards a bulk carrier in the area.
The bulk carrier had recently arrived from Argentina and was a vessel of interest to the AFP.
Two Perth residents and a Lithuanian man have been charged with drug trafficking offences after authorities searched the carrier and found the drugs stashed in packages submerged in a water-filled ballast tank.
Police will allege the three men, aged 21, 25 and 29, had gone out to sea in the cabin cruiser to collect the drugs.
Royal Australian Navy clearance divers retrieved 28 large packages wrapped in blue plastic from the water and another was retrieved once the tank was drained.
Each of the 29 packages contains numerous one-kilogram blocks of a white powdered substance, which forensic tests later confirmed was cocaine.
Investigations continue into any potential involvement of the cargo ship crew.
WA Police Force Assistant Commissioner Tony Longhorn said the bust underscored the importance of intelligence agencies and authorities working together.
"It's not a single agency's responsibility to protect Australia and protect the coast," Mr Longhorn said.
Investigations are continuing into the suppliers and intended distributors of the trafficking attempt.
"It's important that we have both ends of the spectrum covered," Mr Longhorn said.
Two of the men faced court on Thursday while the third man, aged 21, is expected to be extradited from Sydney to Perth.
He is a Lithuanian national who arrived in Australia on May 16.
They face a maximum penalty of life imprisonment if convicted.
