A man sought by police over a mammoth cocaine haul that washed up at a sleepy coastal town in southern Western Australia has allegedly been found hiding under a spa on a back patio in Perth.  

Australian Federal Police said they arrested Mate Stipinovich last night.

The AFP said the 49-year-old also had a loaded gun in a bag beside him when he was found in a secret compartment under the spa in Byford. 

He is in custody over the alleged importation of 365kg of cocaine into WA this year.

Aristides Avlonitis, 36, and Karl Whitburn, 45, have also been arrested and charged by police. 

Esky rescue plot twist 

The trio ran into trouble after their boat capsized in "perilous" waters near Eclipse Island, 17km south of Albany in WA's south, on February 1.

The men were believed to be fishing and set off their EPIRB during the emergency.

The Australian Maritime Safety authority (AMSA) praised the men at the time for having life-saving equipment.

But six days later there was a plot twist when a small, black, plastic-wrapped package washed ashore in the WA tourist town of Denmark.

The AFP said  a seven-metre boat was found overturned in another tourist hotspot town, Peaceful Bay, the next day and was brought to shore by a marine rescue group.

Police said they found another eight similar wrapped packages each containing 40kg of cocaine when they searched the cabin cruiser.

Police believe the drugs were collected from the ocean and loaded onto the boat. 

How and when that happened is still being investigated.

A total of 365kg of cocaine was seized.

All men to face court 

Mr Avlonitis was found at a rural property in Darwin on February 15 and Mr Whitburn was found in Perth's north-east on March 9. 

All three men have been charged with importing a commercial quantity of a border-controlled drug. 

Mr Stipinovich made no application for bail when he appeared in the Perth Magistrates Court this morning.

He was not required to plead to a charge of importing a commercial quantity of a border-controlled drug and was remanded in custody until he faces court again next month.

AFP Sergeant Kristen Swan said her organisation had been working tirelessly to find Mr Stipinovich. 

She said the investigation was ongoing.

The AFP had said it was one of the largest cocaine busts in WA in the past 20 years.