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The Diamond Princess has been docked outside Yokohama under quarantine since February 4 after people on board were found to have been infected with Covid-19.
The total number of virus carriers has now risen to 454, according to Japan's public broadcaster NHK news - nearly 13% of the 3600 people who were on board.
Of those, 85 are passengers and 14 are crew. The health ministry said 19 of the infected people were in serious condition, with some of them in intensive-care units.
NHK reported ministry officials as saying the ship's preventive measures may not be working properly and they needed to work out why the virus was still spreading.
People on board are still being tested, with those whose tests are negative allowed to disembark from Wednesday.
Among the passengers are 11 New Zealanders, who are expected to be evacuated by Australia shortly, along with more than 200 Australians.
While Kiwis have been quarantined on the cruise ship they will be quarantined again when they return home.
Two more Kiwis are in hospital after contracting the virus.
Passengers were due to leave the ship on Wednesday but would have to undergo supervised quarantine when they arrive in New Zealand.
Meanwhile, 300 American cruise liner passengers, including 14 who tested positive for coronavirus, have been flown home to military bases in the United States after two weeks under quarantine.
In New Zealand, director general of health Ashley Bloomfield said Japanese authorities were testing people as they left the boat but quarantine was still needed.
"The issue we are thoughtful about there is if someone is in the early stages of the disease and not symptomatic at all, they may be brewing the infection but not have a positive test,"
The passengers were a higher risk than those who had been evacuated from the disease epicentre of Wuhan because about 10% of people on the boat had contracted the disease, Dr Bloomfield said.
Australian Prime Minister Scott Morrison said a Qantas charter flight would fly the passengers from Japan to Australia on Wednesday.
"We'll also be providing spaces on our flight to New Zealanders, I've been in contact with Prime Minister [Jacinda] Ardern and they welcome that arrangement as well.
"New Zealand passengers will be transferred from Darwin back to their quarantine arrangements in New Zealand."
New Zealand's Ministry of Foreign Affairs and Trade has confirmed the offer.
Consular officials are in close contact with Kiwis on the ship and are working with Australian and Japanese counterparts on the necessary approvals and requirements for those who wish to be evacuated.
Japanese authorities had suggested some passengers might need to stay on board after Wednesday if they had an elevated risk and were not being evacuated by their countries.
Some of the New Zealanders were distressed at that idea but the Government was working to help them, Ardern said.
Otago University epidemiologist Michael Baker said the on-board quarantine was not enough to guarantee the people would be disease free when they arrive home.
"There will be many surfaces on that ship that have viruses on them because there are so many people who were infected. So, as a result, it's very hard to control transmission in that setting," he said.
Meanwhile, the 157 people quarantined at a centre in Whangaparaoa after being evacuated from Wuhan were also due to leave on Wednesday.
The Government is considering whether to keep it ready to continue being used as a quarantine centre.
- Additional reporting RNZ / ABC/ Reuters