One woman was found dead in a rushing stream on the south-western island of Shikoku. A man also died after being swept away by a swollen river in central Japan, the Kyodo News agency reported on Sunday.
More than half a million residents had been ordered to evacuate their homes late on Saturday in western regions where mudslides and flooded rivers were reported.
Authorities warned of high waves, heavy rains and swollen rivers in several areas of the country.
Typhoon Halong made landfall on Aki city on Shikoku at 6am, the Japan Meteorological Agency said.
The eye of the storm was over the Sea of Japan, about 60 kilometres west of Fukui city as of 2pm, travelling north-northeast at 35 km/h, the agency said.
It was packing maximum sustained winds of 108 km/h and gusts of 162 km/h.
Airlines cancelled more than 300 flights scheduled for Sunday in the summer holiday season after about 500 flights were cancelled on Saturday, NHK said.
Many train services, including some bullet trains, have been suspended in western Japan.
Rainfall of up to 300 millimetres was forecast for the Tokai region by Monday noon and up to 250 millimetres for north eastern Japan, the northern island of Hokkaido and Tokyo and its surrounding areas.
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