Sandy Olsen, a spokeswoman for P & O Cruises, which owns the Pacific Star cruise ship, said the woman reported the alleged rape about 4am on New Year's Eve.
The ship was on an eight-day round trip cruise from Auckland and around the Pacific Islands.
The alleged attack happened during a stopover in Lifou Island, near Noumea.
The ship's crew found the 46-year-old female tourist in a state of shock and suffering bruises in the early hours of the morning.
The woman said a 37-year-old Australian passenger had raped her while she was sleeping in her cabin.
Ms Olsen said authorities on the liner immediately contacted French, New Zealand, Australian and British police – as the ship was registered in the United Kingdom.
"We treat all allegations very seriously and we followed our protocols in these sorts of circumstances." She said the cabin was secured to preserve any evidence and support was arranged for the woman.
Ms Olsen said when the ship stopped at Noumea both passengers were given the opportunity to leave the ship, which they did.
The ship arrived back in the country yesterday morning and has since left again on another cruise.
Last July the Pacific Star was in the news after being badly damaged in a storm while carrying 1200 passengers on a cruise – labelled by one passenger as a "holiday from hell" – from Auckland to the Pacific Islands.
Source:RamblerNews