Japan’s weather agency warned of storms and high waves as Typhoon Neoguri skirted the country’s islands of Okinawa, grounding flights and prompting some to flee their homes for emergency shelters.

The warnings were issued as gusts reached 252 kilometers per hour (157 miles per hour), according to the Japan Meteorological Agency. The storm is centered near Okinawa, about 1,500 kilometers from Tokyo, and may reach Kyushu, Japan’s southernmost main island, on Thursday, the agency said.

In the Okinawa city of Miyako, 55,000 residents had been urged to take shelter in community centers and municipal buildings as the storm threatened homes, though only about 30 had complied, disaster prevention spokesman Takezazu Genka said.

Japan Airlines Co. and its affiliates canceled 168 flights to and from Okinawa, affecting about 14,000 passengers, the company said. The All Nippon Airways Co. group scrubbed 110 flights, affecting another 14,000 passengers.

Nansei Sekiyu KK, a unit of Brazil’s Petroleo Brasileiro SA, halted refining and shipping operations yesterday at its 100,000 barrel-a-day Nishihara plant in Okinawa, the company said in an e-mailed statement. Toyota Motor Corp., Nissan Motor Co. and Toshiba Corp., which have factories on Kyushu, said they’re monitoring the storm.

‘Raccoon’

NTT Docomo Inc., Japan’s largest wireless carrier, suffered service outages in several parts of Okinawa, the company said on its website.

“The strength of the typhoon is a once in several decades event,” Akihiro Ohta, Japan’s transport minister, told reporters in Tokyo today. “We urge people to pay attention to warnings from their local governments.”

Neoguri, which means “raccoon” in Korean, was about 100 kilometers west from Kumejima in Okinawa at 2:45 p.m. It had sustained winds of 180 kilometers per hour, making it the equivalent of a Category 3 hurricane on the five-step Saffir- Simpson scale used in the U.S.

Japan has averaged more than 11 typhoons per year over a 30-year period ending in 2010, most of them occurring between July and October, according to the weather agency’s website.

Emergency Warnings

Neoguri was downgraded from a super typhoon by the U.S. Navy Observatory’s Joint TyphoonWarning Center in Pearl Harbor after sustained winds dropped from 204 kilometers per hour.

The storm is forecast to strike Kyushu somewhere between Nagasaki and Kagoshima, said Jim Andrews, a meteorologist with AccuWeather Inc. in State College, Pennsylvania.

“Kyushu is the odds-on favorite to have the worst of the storm,” Andrews said yesterday by telephone. “Whenever you get a tropical cyclone making landfall in Japan you are going to get 10 to 15 inches of rain somewhere, so you get mudslides of course, as well as some flooding.”

Japan has issued storm and high-wave warnings for Okinawa, which has a population of about 1.3 million people and portions of Kyushu.

There are two idled nuclear plants on Kyushu. Because the plants aren’t running, the typhoon is unlikely to cause a release, said Gregory Jaczko, former chairman of the U.S. Nuclear Regulatory Commission. An earthquake and tsunami in March 2011 triggered a meltdown and radioactive release at Fukushima Dai-Ichi plant in the northeast of the country.

‘Been Through Worse’

Kyushu Electric Power Co., which operates the island’s nuclear plants, was monitoring the storm’s approach and would increase safety inspections if it appeared to pose a danger, spokeswoman Naoko Iguchi said.

Neoguri is moving north at 30 kilometers per hour, according to the Japan’s weather agency. The U.S. Navy predicts the storm may come ashore in Kyushu as a Category 2 storm.

Andrews said Neoguri will lose some power as it crosses cooler ocean water in the East China Sea before reaching Kyushu. The storm may cross over Miyakojima, allowing detailed measurements to be taken.

Jeff Schlueter, a U.S. Air Force lieutenant colonel stationed in Okinawa, said the storm had halted most work at his base.

“It’s windy and rainy, but I’ve been through worse,” he said by phone from Kadena Air Base. “I’m from the Midwest, we get tornadoes.”

–With assistance from Yuki Hagiwara, Takashi Amano, Kiyotaka Matsuda, Chris Cooper and Cheng Leng in Tokyo, Mark Chediak in San Francisco, Steven McPherson in Seattle and Brian K. Sullivan in Boston.

*This updated Bloomberg wire story replaces an earlier version.