Pearl Harbor is on Oahu island which is under a Hurricane Warning for the imminent arrival of Category 2 Hurricane Lane.
According to the Navy, ships are sometimes moved out of ports in extreme weather conditions to reduce the risk of damage.
The fleet will remain at sea until the threat passes, and will be positioned to provide assistance if needed.
What the National Oceanic and Atmospheric Administration (NOAA) called “catastrophic flooding” has hit Hawaii’s Big Island as the storm continues to track north.
Will Hurricane Lane hit Pearl Harbor?
Rear Admiral Brian Fort, who commands the Naval Surface Group Middle Pacific, said: “Based on the current track of the storm, we made the decision to sortie the Pearl Harbor-based ships.
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“This allows the ships enough time to transit safely out of the path of the storm.”
Some ships undergoing repairs will remain in port, and crew have taken extra precautions ahead of the storm.
On the current track, the NOAA forecasts the centre of Lane will move dangerously close to portions of the central Hawaiian islands later today and tonight.
A turn toward the west is anticipated on Saturday, with an increase in forward speed.
Some additional weakening is forecast later today and tonight, but Lane is expected to remain a dangerous hurricane as it approaches the islands.
Further weakening is expected on Saturday as the storm heads back out to sea before breaking apart.
Oahu is forecast to take a real beating from the wind and surf brought in by Lane.
In the next 24 hours, 50+ mph wind gusts are forecast and up to 20-foot waves will slam the coast.
Three to five inches of rain will hit – far less than we’ve seen on Big Island, but the wind and surf will be top of the Navy’s concerns as those would cause the most damage to boats tied up in port.
The Hurricane Warning, in place for Oahu and Maui, means that hurricane conditions are expected somewhere within the warning area.
NOAA says the warning is typically issued 36 hours before the anticipated first occurrence of tropical-storm-force winds, conditions that make outside preparations difficult or dangerous.
Other parts of the Hawaii archipelago have Hurricane Watches and Tropical Storm Warnings.
US President Donald Trump declared a state of emergency for Hawaii and ordered federal authorities to aid local emergency responses.
Hawaiian governor David Ige tweeted: “Life threatening flash floods. This is a very dangerous situation. Avoid unnecessary travel.”
NWS meteorologist Chevy Chevalier said: “There’s lots and lots of rain, torrential rain, with a lot of moisture in the atmosphere.
“We’re in it now.”