The ships will head out to sea to get north of the storm and then move east to maneuver around the hurricane, said Adm. Robert J. Natter, commander of the Norfolk-based Atlantic Fleet.
Forecasters said Isabel, with maximum sustained winds of 115 mph, appeared to be on a course to hit Thursday on the North Carolina coast and move up through eastern Virginia.
Natter said moving the ships will cost "in the millions" but the expense would be far greater if the ships were damaged by being battered against the piers.
"We've got to be prudent," Natter told reporters on a pier at Norfolk Naval Station. "We cannot afford to have these very expensive, valuable national assets caught in port in a storm like this."
Natter said Isabel is expected to be especially dangerous because of possible 12-foot surges 500 miles ahead of the eye of the storm.
Most of the ships leaving Tuesday are based in southeastern Virginia. Two Navy oilers were to head to sea from Earle, N.J. More than 13,000 sailors are aboard the ships.