Vessels connected to deep-sea robots equipped with cameras and seismic devices would be among the last to flee and would ride out the rough weather if possible, retired Coast Guard Adm. Thad Allen said.
"If conditions allow, they will remain through the passage of the storm," Allen said in New Orleans.
Bonnie made landfall south of Miami early Friday as a feeble tropical storm with top sustained winds of 40 mph. It broke apart as it crossed Florida and was a tropical depression as it moved into the Gulf, but forecasters expected it to strengthen slightly and roll over the spill site around midday Saturday.
The ships holding the robots would be among the first to return if forecasts force them to leave, but they could be gone for up to two days, said Allen, the federal government's spill chief.
The mechanical plug that has mostly contained the oil for eight days will be left closed, Allen said, but if the robots are reeled in, the only way officials will know if the cap has failed will be if satellite and aerial views after the storm passes show oil pooling on the surface.
Audio surveillance gear left behind could tell BP whether the well is still stable, but scientists won't be able to listen to the recordings until the ships return to the area.
Allen expressed increasing confidence in the experimental cap despite a few leaks that initially worried government experts. Scientists say even a severe storm shouldn't affect the plug, nearly a mile beneath the ocean surface 40 miles from the Louisiana coast.
"There's almost no chance it'll have any impact on the wellhead or the cap because it's right around 5,000 feet deep and even the largest waves won't get down that far," said Don Van Nieuwenhuise, director of professional geoscience programs at the University of Houston.
Crews of other vessels, including one boring the tunnel meant to kill the flow of crude for good, spent Friday pulling up their gear and getting out of the storm's way. Workers were pulling up a mile of pipe in 40-to-60-foot sections and laying it on deck of the drilling rig so they could move to safer water, probably to the southwest flank of the storm.
"Preservation of life and preservation of equipment are our highest priorities," said Allen, a veteran of the Coast Guard's rescue mission after Hurricane Katrina.
Shell Oil was also evacuating its operations in the Gulf, moving out more than 600 workers and shutting down production at all but one well sheltered safely in Mobile Bay.
At the spill site, the water no longer looks thick with gooey tar. But the oil is still there beneath the surface, staining the hulls of boats motoring around in it.
Strong winds and waves could help break up the oil further, but a storm surge also might push it into sensitive marsh areas along the coast.
"Those are two opposite consequences and we're prepared to move out and aggressively attack this once the threat has passed through," he said.
The foul weather has stalled progress toward killing the well and could delay until mid-August the sealing of the nearly two-mile underground shaft using mud and cement, Allen and BP say. BP had hoped to finish drilling a relief tunnel Friday, but had to plug it Wednesday to prepare for the storm.
Before the cap was attached and closed a week ago, the broken well spewed 94 million to 184 million gallons into the Gulf after the BP-leased Deepwater Horizon rig exploded April 20, killing 11 workers.
BP is likely to be fined per gallon spilled, although determining that could be difficult. Concentrations of underwater oil at least doubled last month, according to the National Oceanic and Atmospheric Administration.
Researchers at the University of South Florida said Friday they have the first scientific proof that two giant plumes of oil beneath the surface of the Gulf came from the broken well. BP initially denied the plumes even existed.
Dishneau reported from New Orleans, Weber from aboard the Coast Guard cutter Decisive. Associated Press writers Jason Dearen in San Francisco and Matthew Brown in Billings, Mont., contributed to this report.