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Man found clinging to esky off West Australian coast, before cocaine-filled boat washed ashore, extradited from Darwin to Perth

Police say Aristides Avlontis was among the men rescued before they were found to allegedly be connected to the drugs.  (Supplied: AFP)

A Northern Territory man who police allege is connected to a cocaine-filled boat that capsized off south-west Western Australia will be extradited to Perth to face drug importation charges. 

Aristides Avlonitis, 36, was arrested on Wednesday at a property in Darwin's rural area, days after Australian Federal Police (AFP) launched a manhunt for three men who were found clinging to an esky off the Western Australian coast two weeks ago. 

At the time of the rescue, authorities believed the trio had been fishing when the boat capsized near Eclipse Island and they activated a distress beacon.

A week later, the AFP linked the men to an alleged drug trafficking operation when the boat that police allege they were on washed ashore in Peaceful Bay. 

A number of packages were found on the boat, while another washed ashore about 50km away in the town of Denmark, allegedly containing 365 kilograms of cocaine.

Police described the discovery as one of the largest cocaine busts in Western Australia in the past 20 years. 

Aristides Avlonitis (centre) was arrested in Darwin, while police continue to search for Mate Stipinovich and Karl Whitburn.  (Supplied: AFP)

Officers say they believe the drugs were collected from the ocean, but how and where they were dropped in the water is still under investigation.

Mr Avlonitis had travelled back to Darwin and is the first of the three wanted men to be arrested. He appeared in the Darwin Local Court on Thursday.

AFP officers wanted the accused brought to WA to face a charge of importing a commercial quantity of a border-controlled drug.

The boat was retrieved by police, who say the drugs were onboard.  (Supplied: AFP)

Commonwealth prosecutor Christine Wilson told the court Mr Avlonitis would remain at the Palmerston police station until he could be taken to Perth, which would occur no later than Friday.

Mr Avlonitis' lawyer, Josh Begbie, did not oppose the application for extradition.

The 36-year-old appeared in person and was supported by members of his family, who sat in the public gallery.

Police say they are still searching for 49-year-old Mate Stipinovich and 45-year-old Karl Whitburn, who they believe are in Western Australia.

"We are also appealing for anyone else to call us if they have information to help us find the men, or know anything about this drug importation," AFP Acting Commander Graeme Marshall said in a media release.

"The interception of this amount of drugs would be a significant blow to a well-resourced syndicate and prevents millions of dollars of drug profit from flowing back into the group to fund their next criminal venture or lavish lifestyles."

Police say they believe the 365kg seizure was destined for distribution across the country.

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