TOKYO (Reuters) - A super typhoon described as a "once in decades storm" was heading north for Japan on Monday, set to rake the southern Okinawa island chain with heavy rain and powerful winds before making landfall on Kyushu, Japan's westernmost main island.

Typhoon Neoguri was already gusting at more than 250 km an hour (150 mph) and may pick up still more power as it moves north, growing into an "extremely intense" storm by Tuesday, the Japan Meteorological Agency (JMA) said.

But it was not expected to be as strong as Typhoon Haiyan, which killed thousands in the Philippines last year.

The storm was south of Okinawa but moving northwest at 20 kph (12 mph) with sustained winds of 180 kph (110 mph), the JMA said on its website, warning of high tides and lashing rain.

"This storm's characteristic is its strength," one JMA official said, calling on people in Okinawa to evacuate early and take precautions, including staying indoors. Television showed fishermen winching their boats out of the water.

There are no nuclear plants on Okinawa, but there are two on Kyushu and one on Shikoku island, which borders Kyushu and could also be affected.

All are halted in line with current national policy. A spokeswoman at Kyushu Electric Power Co said there are no specific plans related to this typhoon but that the company has plans in place throughout this year to protect the plants from severe weather.

The Fukushima Daiichi nuclear plant, crippled by an earthquake and tsunami in 2011, is on the other side of the country, which is likely to see rain at the worst.

The commander at Kadena Air Base, one of the largest U.S. military establishments on Okinawa, which hosts the bulk of the U.S. forces in Japan, warned that damaging winds were expected by early Tuesday.

"I can't stress enough how dangerous this typhoon may be when it hits Okinawa," wrote Brigadier General James Hecker on the base's Facebook page on Sunday. "This is not just another typhoon."

Though officials warned that parts of western Japan were likely to be hit by torrential rain, Tokyo was likely to be spared the brunt.

Around two to four typhoons a year make landfall in Japan but they are unusual in July.

(Reporting by Elaine Lies; Editing by Nick Macfie)