An extraordinary two-week quarantine of the Diamond Princess cruise ship ends Wednesday, with thousands of passengers and crew set to disembark over the next several days in the port of Yokohama, near Tokyo.

A growing number of scientists, however, say the ship served as an incubator for a worrisome new virus from China instead of a quarantine facility meant to prevent the worsening of an outbreak that has sickened tens of thousands.

As of Tuesday, 542 cases of the virus have been identified among the 3,711 quarantined passengers and crew, making the ship the site of the most infections outside of China.

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The question now is: Why?

The Japanese government has repeatedly defended the effectiveness of the quarantine. But some scientists suggest that it may have been less than rigorous.

In a possible sign of lax quarantine protocols, three Japanese health officials who helped in the quarantine checks on the ship were also infected.

“I suspect people were not as isolated from other people as we would have thought,” said Dr. Paul Hunter, a professor of medicine at the University of East Anglia in England.

Japan’s health minister, Katsunobu Kato, told reporters Tuesday that all passengers who remained on the cruise ship have had their samples taken and that those who tested negative would start getting off the vessel beginning Wednesday, when their required 14-day quarantine is scheduled to end.

“They all want to go home as early as possible, and we hope to assist them so that everyone can get home smoothly,” Kato said.

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The process is expected to take until Friday because of the large number of people involved.

“Obviously the quarantine hasn't worked, and this ship has now become a source of infection,” said Dr. Nathalie MacDermott, an outbreak expert at King's College London.

She said the exact mechanism of the virus' spread was unknown.

“We need to understand how the quarantine measures on board were implemented, what the air filtration on board is like, how the cabins are connected and how waste products are disposed of,” MacDermott said.

“There could also be another mode of transmission we're not familiar with,” she said, noting the possibility of environmental spread and the importance of “deep-cleaning” the entire ship to prevent people from touching contaminated surfaces.

During the 2002-2003 outbreak of SARS, a related virus, experts discovered that more than 300 people were infected through a defective sewage system in a Hong Kong housing estate. MacDermott said it was possible there was a similar issue aboard the Diamond Princess, but that a full investigation was needed.

“There's no reason this should not have worked if it had been done properly," she said.

Some passengers on the Diamond Princess described the ship as a “floating prison” but were allowed to walk on the decks every day while wearing a mask and were told to keep their distance from others.

Hunter, the medicine professor, said the continued spread of the virus could be due to compliance problems.

“It's difficult to enforce a quarantine in a ship environment and I'm absolutely sure there were some passengers who think they're not going to let anyone tell them what they can and cannot do,” he said.

Hunter said it was “a huge disappointment” that the quarantine hadn't curbed the spread of the virus and that it was unfortunate some passengers returning to their home countries would now face a second period of isolation.

“Given how the virus has continued to spread, we have to presume everyone leaving the ship is potentially infected, and therefore they have to go through another two-week quarantine period,” he said. “Not to do so would be reckless.”

Japanese health officials say a 14-day quarantine on the ship is adequate, citing results that all but one of more than 500 Japanese returnees from Wuhan, the epicenter of the virus in China, who initially tested negative were also found to be virus-free at the end of their 14-day quarantine at government facilities.

Those officials also have defended precautions taken on the ship. About 1,000 crew members were told to wear surgical masks, wash their hands, use disinfectant sprays and stop operations at restaurants, bars and other entertainment areas after Feb. 5, when the first group of 10 infected people was reported and the official start of the 14-day quarantine was announced.

Dr. Michael Ryan, the chief of emergencies at the World Health Organization, said earlier this month that the agency was working with Japanese officials to help passengers get off the ship as soon as possible.

“It's really important that there's an appropriate risk management approach being taken here,” he said last week. He reminded countries of their obligations to respect the human rights of travelers and said they were working to ensure that “we don't end up with an unfortunate consequence of people having to stay too long in that situation.”

Passengers were instructed to stay in their cabins and not walk around or contact other passengers. Those in windowless cabins could go out on the deck to take a walk or exercise for about an hour each day.

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The two-week quarantine was largely for the passengers, because crew members kept sharing double rooms with their colleagues, and they continued to serve the guests by delivering food, letters, towels and amenities, and entering passenger cabins for cleaning. Crew members also cooked their own food and ate in groups in a crew mess hall.

“Unlike passengers, crew members share their rooms, they share food, and that’s why some of them are infected even after the quarantine started,” Shigeru Omi, a former regional director for the World Health Organization, said at a recent news conference.

Omi said quarantine is one of the measures considered effective early on. But the virus has already made its way into local communities across Japan, where untraceable cases have been popping up already, he said.

At this stage, “the spreading of the virus will be inevitable, and that’s why quarantine is out of the question,” Omi said.

He said the focus now should shift from border control to preventing the spread in local communities.

Other scientists said that passengers should have been removed from the boat from the beginning.

“Boats are notorious places for being incubators for viruses,” said Arthur Caplan, a professor of bioethics at the New York University School of Medicine. “It's only morally justified to keep people on the boat if there are no other options."

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Caplan said that a second quarantine was justified, but that officials had done a poor job of explaining from the outset what would happen if their original plan failed.

“It's never good to lose your civil liberties and your rights of movement, but two more weeks of quarantine is not an undue burden if you're trying to protect spread of a disease,” he said.