Japan's weather agency issued its highest alert as super typhoon Neoguri barreled towards the southern Okinawa island chain on Monday, with 55,000 people urged to evacuate as officials warned of one of the worst storms in decades.

The top-level warning means a threat to life, as well as the risk of massive damage from torrential rains and gusts of up to 270 kilometres (160 miles) per hour.

The Japan Meteorological Agency issued the alert for Okinawa's main island, home to around 1.2 million people, as well as the outlying Miyako islands, where all 55,000 residents were ordered to evacuate.

"We advised all 55,000 people in Miyako at 10:00 pm (1300 GMT) to evacuate to facilities such as community centres and municipal buildings," Miyako disaster official Katsuhiro Koja told AFP by telephone.

The biggest US Air Force base in the Pacific, located on Okinawa's main island, evacuated some of its aircraft as officers stressed that Neoguri may be deadly.

Waves could reach as high as 14 metres (45 feet), a weather agency official said in a warning that was likely to revive memories of Japan's quake-tsunami disaster in 2011.

The typhoon was some 500 kilometres (310 miles) south of the main Okinawan island at 1200 GMT and was moving north northwest at 25 kilometres (16 miles) per hour.

Miyako, in the centre of the archipelago, was in the expected path of the massive storm.

"Record-level violent winds and high waves are posing a serious danger to the Miyako island region," Satoshi Ebihara, the weather agency's chief forecaster, told an evening news conference.

"People are advised to refrain from going outdoors... evacuate if necessary before violent winds occur and take appropriate action to protect themselves," he said.

The massive gusts and torrential rains will possibly reach mainland Japan by Wednesday, a weather agency official said earlier Monday.

- Evacuation order -

The meteorological agency forecast Neoguri -- whose name means "racoon" in Korean -- would dump up to 80 millimetres (three inches) of rain an hour on Okinawa as it pounds the archipelago.

The storm, which could affect an area with a 500 kilometre radius, was expected to be downgraded by the time it hit the mainland.

However, the Kyushu region -- next to the main island of Honshu where major cities including Tokyo and Osaka are located -- was already seeing heavy rain and officials warned of possible floods and landslides.

"I'm calling on the heads of municipalities not to hesitate in issuing evacuation warnings and don't be afraid of being overcautious," Keiji Furuya, the state minister in charge of disaster management, told a government meeting.

The US Kadena Air Force base in Okinawa, the largest US airbase in the Pacific, began evacuating some of its aircraft Sunday in preparation for the typhoon.

"I can't stress enough how dangerous this typhoon may be when it hits Okinawa," Commander James Hecker of the 18th Wing stationed in Kadena said in a statement posted online.

"This is the most powerful typhoon forecast to hit the island in 15 years; we expect damaging winds to arrive by early Tuesday morning.

"So be prepared!" Hecker said. "Tie down your outdoor items and work with your neighbours to help them."

He added: "During the typhoon, do not go outside... anything not tied down, even small items, could become deadly projectiles."

Okinawa is regularly hit by typhoons but islanders were taking no chances, with Miyako fishermen bringing boats back to port and tying them down.

"It's rare that we brace for a typhoon (as early as) July," one fisherman said.