AFP acting assistant commissioner David Sharpe said the United States Drug Enforcement Agency (DEA) tipped them off in August that an organised crime syndicate had launched the vessel from Ecuador headed for Australia.
The AFP and Tongan and Cook Islands police were able to track the yacht's journey but lost contact after it left the Cook Islands.
Mr Sharpe said the dead body was so decomposed the initial post-mortem examination had difficulty in identifying a cause of death.
Australian forensic experts were assisting Tongan authorities with this process, he said.
Mr Sharpe said police teamwork spanning a network of nine Pacific countries helped "put a net around the vessel" and was ensuring criminal gangs were not exploiting "vulnerabilities" in the Pacific.
The operation was an "outstanding" example of global and regional police co-operation, he said, as investigations continued across four countries.
"I think the health implications of $116 million of cocaine, 200 kilos, are quite significant," Mr Sharpe told reporters at the AFP headquarters in Canberra.
"This is the fourth vessel since 2010 targeting Australia - a total of 1.1 tonnes of cocaine on four yachts that have been stopped."
Mr Sharpe dismissed claims the drug seizure was a fluke because the yacht had become stranded.
He heaped praise on the efforts of Cook Islands and Tongan authorities.
US DEA spokesman David Cali said authorities believed they knew the identities of two people who were on the boat when it left South America.
Mr Sharpe was tightlipped about whether the second person was likely to be still alive.
Customs and Border Protection spokesman Neil Sugget said despite significant customs resources being tied up on the west coast searching for asylum seeker boats he was confident the agency could protect Australia's east coast from drug smugglers.
"We use a combination of forward planning, if we have got intelligence we can move vessels ... and we get assistance from NSW and Queensland police, so there are resources available," he said.
- AAP