Elsewhere in the Pacific, a separate typhoon whipped the Mariana Islands, including Guam, with high winds and heavy rain.
In Japan, bullet train service was suspended between Tokyo and Osaka because of heavy rain, and more than 600 flights were cancelled at Tokyo's Haneda Airport.
Typhoon Phanfone came ashore near the city of Hamamatsu shortly after 8 a.m. Authorities issued evacuation advisories for more than 400,000 people in the storm's path.
One of the three airmen was found dead. The other two were missing, according to the Air Force and the Japanese coast guard.
They had been on Okinawa island's northern coast when they were overcome by the waves, according to Tsuguyoshi Miyagi of the coast guard's Okinawa branch.
The Air Force said the search for the missing airmen had been interrupted by rough seas. Their names were being withheld pending notification of relatives.
Okinawa is home to about half of the roughly 50,000 American troops stationed in Japan.
Japanese Grand Prix cut short by storm
Several people on Kyushu island were injured in the typhoon. The storm also grounded more than 100 flights Sunday and knocked out power to more than 9,500 Kyushu homes.
In Suzuka, in central Japan, a French driver was severely injured following an accident in the Japanese Grand Prix that had to be shortened because the heavy rain made conditions too dangerous. Formula One driver Jules Bianchi of the Marussia team went off the track at a turn and hit a recovery vehicle that was removing a car that had crashed earlier.
An unconscious Bianchi was taken to a nearby hospital where he underwent emergency surgery for a severe head injury. Race officials said he was in critical condition.
The storm triggered concern about possible landslides on the ash-covered volcano in central Japan that erupted Sept. 27 and killed at least 51 hikers. The search for a dozen people missing in the eruption was suspended Sunday because of rain from the approaching storm.
The meteorological agency predicted that up to 40 centimetres of rain could fall in central Japan by Monday morning.
Guam hit by separate typhoon
In the Marianas, the eye of the typhoon skirted the small island of Rota. Power outages and minor flooding were reported in some areas on Monday morning as damage reports were starting to arrive.
Rota has about 2,500 residents and many buildings made of concrete.
The weather service cancelled a flash-flood watch for the islands around 8:30 a.m. Monday, as the storm shifted farther west. Light to moderate rain was expected to continue for several hours, with occasional downpours, but major flooding wasn't expected, the agency said.
Typhoon Vongfong had maximum sustained winds estimated at 169 km/h, said Roger Edson of the National Weather Service in Guam.
Winds on the islands of Guam, Tinian and Saipan were gusting to at least 89 km/h, he said.
Residents on Guam heeded warnings about high winds and possible flooding by taking shelter at designated public schools. The island government and many businesses were expected to be closed Monday, and most flights were cancelled.