Sailors on a US nuclear warship where dozens of crew have been diagnosed with coronavirus are now being evacuated and put into quarantine, navy top brass have said.

The USS Theodore Roosevelt - which has 5,000 people on board - docked in Guam earlier this week with the aircraft carrier's captain warning that the onboard infection could be fatal if he did not receive help.

"We are not at war,” Caprain Brett Crozier wrote in a four-page letter to bosses detailing how the ship did not have enough quarantine facilities. “Sailors do not need to die. If we do not act now, we are failing to properly take care of our most trusted asset – our sailors.”

Now, his demand to get crew ashore appears to have been met with Acting Navy Secretary Thomas Modly confirming sailors were being taken off board in stages, with 1,000 people already evacuated and placed in isolation on land.

It is thought around 100 people on the nuclear-powered vessel have tested positive for Covid-19, although this remains unconfirmed by the navy itself.

Modly said the force had been working for several days to get the majority of crew off the ship but that, because Guam was dealing with its own outbreak of Covid-19, there were not currently enough isolated beds. He said he was in talks with officials there to use hotels and set up tents.

“It’s not the same as a cruise ship, it has armaments on it, it has aircraft on it, we have to be able to fight fires if there is a fire on there,” he said.

“There are a lot of things that we have to do on that ship that make it a little bit different and unique but we’re managing it and we’re working on it and we’re taking all the input and we appreciate all the input from the chief officer on the ship and the medical officer on the ship and we’re going to work on those issues immediately.”

And he added: “The Navy and marine corp team, we all have one mission: to defend the nation. We have a responsibility to protect the seas, to protect our friends and allies around the world.

“It's key to make sure that we get a set of crew members who can man all the machines and make sure they’re clean and get them back on while we clean the ships and get the other crew members off.

“We’re accelerating it as we go. I think there are things that are happening in the past 24 hours that come after the comments from the chief officer. We’re in constant communication with that ship.”

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Admiral John Aquilino, head of the US Navy’s Pacific Fleet, told reporters separately that the plan was to take some sailors off the ship, test and quarantine them, clean the vessel and then rotate them with those on the carrier.