Police have charged a man over what's been dubbed one of the largest cocaine drug busts in Western Australia's history.

Australian Federal Police (AFP) revealed yesterday they were searching for three men after 365 kilograms of cocaine was allegedly found in packages inside a capsized vessel on a beach on WA's south coast last week.

A 36-year-old man was arrested at a home in Darwin this morning and is due to appear in court on Thursday.

The AFP said it would apply for an extradition to WA to face a charge of importing a commercial quantity of a border-controlled drug.

Police continue to search for two other men linked to the seizure.

Three men were rescued from the ocean after they were found clinging to an esky on February 1 in the ocean off Albany.

The trio's boat had capsized and started sinking.

A week later AFP said it discovered six suspicious packages on the capsized boat, which washed ashore near Peaceful Bay, about 80km west of Albany.

A similar package was discovered on a beach in Denmark.

Police want to speak to two men aged 49 and 45, who are believed to be in WA.

One of them is the registered owner of the boat where the illicit drugs were found.

AFP Acting Commander Graeme Marshall urged 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.