Many appeared to be in high spirits, waving and giving thumbs up signs as they walked from the terminal wearing face masks.
"We've still had a fantastic time, and I think the crew on the ship and most passengers have all looked at it with glasses half full," a Brisbane woman, who gave her name only as Tania, told Australian Broadcasting Corp.
The passengers were not allowed to disembark at islands and resorts in the coral reefs off the tropical Queensland coast after it emerged passengers from a previous sailing had tested positive for swine flu.
When three crew members aboard the ship also tested positive for the virus Thursday, the 10-day journey north was aborted.
Seven passengers who exhibited flu-like symptoms were tested as well for the disease that has killed 100 people worldwide, but all were cleared before the ship docked in Brisbane, Queensland's chief health officer Jeannette Young said.
"While this is a comforting result, it is not time to drop our guard," she said in a statement.
Queensland state Health Minister Paul Lucas declared a medical emergency early Saturday to force the cruise terminal manager, Brookfield Multiplex Ltd., to allow the ship to dock.
"It was necessary to ensure the cooperation of the port operator as they were reluctant to allow the vessel to berth here," Lucas told reporters.
Brookfield Multiplex spokeswoman Kerrie Muscens declined to detail the company's concerns about the Pacific Dawn to The Associated Press. But she said the company had cooperated fully with the government and health authorities.
New South Wales state authorities, based in Sydney where the ship's journey began, have come under fire for their handling of the incident.
Officials have been criticized for allowing the Pacific Dawn to sail Monday before test results on passengers and crew from the previous week's cruise were known. The three crew who tested positive had been on the first cruise as well.
