Engineers had feared earlier that the cap that has mostly contained the oil in the last week would have to be reopened and left gushing if a major storm came through.
But after days of tests, they were confident enough now in the strength of the cap to leave it sealed while most support ships left the area.
Tropical Storm Bonnie raked the low-lying Turks and Caicos Islands and the Bahamas with rain and lightning on Thursday, and forecasters at the US National Hurricane Center said the storm could reach the Gulf of Mexico by Saturday. The storm is expected to cross over the site of the spill.
Scientists say even a severe storm shouldn't affect the well cap, nearly a mile (1.6 kilometers) beneath the ocean surface 40 miles (65 kilometers) from the Louisiana coast.
"Assuming all lines are disconnected from the surface, there should be no effect on the well head by a passing surface storm," said Paul Bommer, professor of petroleum engineering at University of Texas at Austin.
Still, it could delay by another 12 days the push to plug the broken well for good using mud and cement, retired Coast Guard Adm. Thad Allen and BP officials conceded.
"While this is not a hurricane, it's a storm that will have probably some significant impacts, we're taking appropriate cautions," Allen said in Mobile, Alabama.
Bonnie had maximum sustained winds near 40 mph (65 kph) Friday morning as it swirled about 80 miles (130 kilometers) southeast of Miami.
A broken oil well has spewed somewhere between 94 million gallons and 184 million gallons (356 million liters and 697 million liters) into the Gulf before the cap was attached a week ago. The crisis - the biggest offshore oil spill in US history - unfolded after the BP-leased Deepwater Horizon rig exploded April 20, killing 11 workers.
Some experts worry the hurricane season could worsen environmental damage from the spill, with powerful winds and large waves pushing oil deeper into estuaries and wetlands and also depositing more of the pungent, sticky mess on beaches.
Allen said forcing ships to move out could leave the well head unmonitored for up to a few days, and he ordered BP to make sure the ships carrying the robotic submarines watching the well were the last to leave and the first to return.
Allen issued the order Thursday night to begin moving dozens of vessels from the spill site, including the rig that's drilling the relief tunnel engineers will use to permanently throttle the free-flowing crude near the bottom of the well. Some vessels could stay on site, he said.
"While these actions may delay the effort to kill the well for several days, the safety of the individuals at the well site is our highest concern," he said.
It was not yet clear whether the ships would go back to port or head farther south in the Gulf out of the path of the storm. The Coast Guard cutter Decisive, the hurricane guard for the vessels at the spill site, was awaiting instructions. It will be the last vessel to leave the area.
Bonnie caused flooding in Puerto Rico, the Dominican Republic and Haiti before reaching tropical storm strength.
Seas already were choppy in the Gulf, with waves up to five feet (1 1/2 meters) rocking boats as crews prepared to leave, and smaller boats involved in the coastal cleanup were called into port, Coast Guard Rear Adm. Paul Zukunft said.
Louisiana Gov. Bobby Jindal said he expects local coastal leaders to call for evacuation of low-lying areas later Friday.
At the spill site, the water no longer looks thick with gooey tar. But the oil is still there beneath the surface, staining the hull of ships motoring around in it.
One large vessel - the Helix Q4000 - is burning off oil collected from the water, and bright orange flames flared at the side of the ship.
Charles Harwell, a BP contractor monitoring the cap, was confident.
"That cap was specially made, it's on tight, we've been looking at the progress and it's all good," he said after his ship returned to Port Fourchon, Louisiana.
Work on plugging the well came to a standstill Wednesday, just days before authorities had hoped to complete the relief shaft. Allen said he has told BP to go ahead preparing for a second measure called a static kill, which would pump mud and cement into the well from the top, a move he said would increase the relief well's chances for success. BP will have to get final approval from Allen before starting the procedure.
