Emergency services were called to a marina in Balmain just after 4pm on Saturday following reports a woman was found unconscious on a boat.
She was treated by paramedics but was unable to be revived, police said in a statement.
Police and paramedics remain at the marina and a crime scene has been established.
It was too early to tell whether the incident was suspicious or not, and police were looking at the situation from all angles, a spokeswoman said.
A paramedic told reporters up to 100 people could have possibly been on board the cruise ship, which had been hosting a birthday party.
"She appears to have collapsed in the toilet where we found her and we have extricated her out from there to the back deck," he said.
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