Officers from the Australian Border Force (ABF), with the help of sniffer dogs, searched the ship's passenger cabins on Sunday and allegedly found 95 kilograms of the drug packed into suitcaseses.
Andre Tamine, 63, Isabelle Legace, 28, and Melina Roberce, 23, faced charges of importing a commercial quantity of cocaine when they appeared in court today.
They appeared in Sydney's Central Local court via video link from police custody.
The trio did not apply for bail and it was formally refused. They will remain in custody until their next appearance on October 26.
The maximum penalty for drug importation is life imprisonment.
The ABC understands the ship in question is the Sea Princess, part of the Princess Cruises fleet.
The Australian Federal Police (AFP) said the operation was undertaken in cooperation with the US Department of Homeland Security Investigations, the New Zealand Customs Service and the Canada Border Services Agency.
ABF Assistant Commissioner for Strategic Border Command, Clive Murray, said the operation was another example of international cooperation leading to significant results in the fight against international drug syndicates.
"These syndicates should be on notice that the Australian Border Force is aware of all the different ways they attempt to smuggle drugs into our country and we are working with a range of international agencies to stop them," he said.
The AFP said investigations remained ongoing and they had not ruled out further arrests.
Princess Cruises' owner Carnival said it provided full support to authorities during the police operation.