"It could have been worse," Avila said. "They were very, very lucky."
Hurricane Omar had maximum sustained winds of 125 mph (205 kph) but a last-minute shift to the east meant that St. Croix, the most populated of the U.S. Virgin Islands, experienced the weaker side of the system. Winds there reached just 48 mph (77 kph) mph, officials said.
The storm knocked down trees, caused some flooding and minor mudslides but there were no immediate reports of deaths or major damage, said Mark Walters, director of the U.S. Virgin Islands disaster management agency.
The nearby British Virgin Islands also emerged largely unscathed, said Deputy Gov. Inez Archibald, noting there was little damage beyond some mudslides and scattered debris.
"We did reasonably well actually," Inez told The Associated Press. "We did not get what we expected."
At 5 a.m. EDT Thursday, Omar's center was located about 70 miles (110 kilometers) north of St. Martin. It was moving northeast near 25 mph (41 kph).
Omar was taking an unusual southwest-to-the-northeast track toward the central North Atlantic, well away from the U.S. mainland.
On the Puerto Rican island of Vieques, the storm flooded roads and downed tree branches. Fishermen and others gathered at dusk to watch the rough surf smash against a seawall.
One death was reported on Puerto Rico's tiny island of Culebra. Authorities say a 55-year-old man collapsed from cardiac arrest while trying to install storm shutters on his house.
Many people throughout the islands had feared the worst and spent Wednesday securing their homes and making sure they had enough food, water and batteries.
"I plan to stay up all night and ride out the storm, but I have a feeling it's going to be very bad," said St. Croix resident Helino Cruz, retiree from the island's giant Hovensa oil refinery.
The refinery, one of the 10 largest in the world, shut down operations for the storm. Hovensa was expected to conduct an inspection for any damage before deciding whether to restart the refinery.
Hurricane Omar forced at least three cruise ships to divert course. Flights were canceled on several islands.