The 13-metre yacht JeReVe left Ecuador in August, laden with 204 one-kilo blocks of cocaine which authorities believe was destined for the Australian market.
Police forces from Australia, Tonga and the Cook Islands, along with the US Drug Enforcement Administration (DEA), lost contact with the vessel on October 5.
Tongan authorities discovered the boat after an alert was sent out to the Pacific Transnational Crime Network by Cook Islands police, who had been monitoring the boat.
The Australian Federal Police says the vessel was found washed up on the isolated atoll of Luatafito, 10 nautical miles off the capital of Tonga, on November 5.
AFP Acting Assistant Commissioner David Sharpe said the operation was a great example of the global reach of law enforcement.
"Whilst we can state that those drugs were not destined for Tonga or the Cook Islands, Tonga and Cook Islands played an integral part of this investigation," he said.
Mr Sharpe said the seizure of the drugs stopped approximately $116 million worth of cocaine from reaching Australia's shores.
Police say the dead body was badly decomposed and an initial post-mortem could not determine the cause of death.
US authorities say they believe there were two men on board the boat when it left South America, and that they know who the men were.
The Pacific Transnational Crime Network has been involved in three similar drug seizures in the past two years, including a 400 kilogram haul of cocaine coming from Vanuatu under the cover of a yacht race.
Tonga's Police Commissioner, Grant O'Fee, told Radio Australia's Pacific Beat the seizure was "very significant."
'It's great to have that amount of cocaine out of circulation because it's a lot of misery for a lot of people that's been removed from circulation," he said.