The Japan Meteorological Agency warned of mudslides, high waves and swollen rivers on the southern island of Kyushu and the south-western island of Shikoku.
Halong, the 11th typhoon of the season, was projected to make landfall on one of the two islands late Saturday.
As of 6 pm (0900 GMT), the eye of the storm was 210 kilometres east of Amami Oshima Island, travelling north at 15 kilometres per hour, the agency said.
The typhoon had maximum sustained winds of 144 kph and gusts of 198 kph, the agency said.
Rainfall of up to 500 millimetres was forecast for Shikoku by Saturday evening, up to 400 millimetres for Kyushu and the Kinki region and up to 200 millimetres for the nearby Tokai region.