Japan's weather agency said Tuesday "very strong" typhoon Hinnamnor was nearing several remote southern islands, prompting warnings for local residents to seek shelter before it becomes too dangerous.

On Tuesday evening, the typhoon was in Pacific waters south of Japan, 340 kilometres (210 miles) east-northeast of Minami Daito island, one of a string of remote isles that form the Okinawa region, according to the Japan Meteorological Agency.

Packing gusts up to 252 kilometres per hour, it was moving west at a speed of 30 kilometres per hour, and is expected to threaten the islands from Wednesday evening through Friday.

Some of the islands are remote with only several hundred residents, but the region as a whole has around 1.4 million people, and the Okinawa mainland hosts most of the US military bases in Japan.

The weather agency expects the storm will strengthen to its top category "violent" from Wednesday evening, with gusts up to 270 kilometres per hour.

The intense winds from Wednesday may cause "some houses to collapse", the Okinawa unit of the national weather agency said.

Heavy rain and high waves will also hit the region.

"Please exercise serious caution for violent wind. Take precautionary steps such as moving to strong buildings before strong winds begin," the agency said.

Japan is currently in typhoon season and is hit by around 20 such storms a year, routinely seeing heavy rains that cause landslides or flash floods.