The FBI boarded the cruise ship in Juneau. It was carrying 3400 passengers and 1100 crew members and it docked in the Alaskan capital overnight after the ship alerted passengers to the news surrounding the 39-year-old's death.
The ship, a Sydney-based liner operated by Princess Cruises and part of Carnival Australia, diverted to the city after the woman's body was found.
Her identity has not yet been revealed but federal officials say they plan to announce the filing of charges in the woman's death.
The death occurred in US waters off the coast of Alaska on Tuesday night around 9pm.
Passengers told America's ABC News they were in lockdown and the captain had ordered passengers in decks 8, 9 and 10 on the port side to be interviewed by police.
The ship departed Seattle on Sunday for a week-long trip that was cut short by the incident.
Before the bulk of the passengers were allowed off the ship, a smaller group of passengers were seen exiting in two groups wearing "white and grey hooded sweatshirts".
"The hoods and umbrellas obscured their faces," reported the Washington Post.
"The groups were taken to vehicles with dark-tinted windows waiting in a restricted area of the port, and the people were whisked away."
A passenger was detained by the crew, the cruise liner said, adding the ship had authority to detain a person who commits a crime.
A Princess Cruises spokeswoman would not confirm if passengers would be offered compensation but said "conversations" were taking place.
"Our thoughts and prayers are with the family and all those impacted by this tragic event," Princess Cruises said in a statement.
Spokesperson Negin Kamali declined to comment on any further details of the case and referred all questions to the FBI.
One passenger told news.com.au it seems "more people were bummed they were confined to the ship all day and missed their expensive tours".
"But I got the impression they had whoever was involved quickly."
One passenger tweeted "very frightening being on the Emerald right now - people are upset and don't know what to do".
Another said they were being "held hostage".
- Additional reporting by Associated Press
