Aristides Avlontis, 36, was arrested at a home in Darwin yesterday and he is due to appear in court later today.
Police allege they found 365kg of cocaine in a nearby vessel and washed up onshore in southern WA.
The Australian Federal Police said they will apply to extradite Avlontis to WA to face a charge of importing a commercial quantity of a border controlled drug.
Three men were rescued from the ocean after they were found clinging to an esky on February 1 in the sea off southern WA.
The trio told police their boat capsized while they were fishing off the Albany coast when they were pulled from the water after sending a distress signal.
Six days later, a black package containing multiple packages of cocaine washed ashore near Denmark, 423kms south-east of Perth.
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The AFP said a seven-metre boat was also found overturned off Peaceful Bay the following day with more cocaine inside.
Police are continuing the search for Mate Stipinovich, 49 and Karl Whitburn, 45, who are believed to be in Western Australia.
One of them is the registered owner of the boat where the illicit drugs were found.
AFP Acting Commander Graeme Marshall calle on the men to hand themselves in.
“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,” he said.
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