Prime minister Shinzo Abe warned the typhoon could bring "record rains, winds, waves and high tides".
The typhoon hit with winds of up to 120 kph and gusts of 150 kph, heavy rain and flooding.
Residents across large parts of the south east were woken in the night by a "huge bang", causing fears of an explosion.
Six million people have been advised to evacuate.
Thousands of train commuters in Hong Kong experienced severe overcrowding and disruption, as the city returned to work just a day after it was battered by Typhoon Mangkhut.
The victims died mostly in landslides and houses that got hit by the storm's fierce winds and rain.
Passengers were marooned after a tanker hit a bridge.
'You can almost sense it’s power from 250 miles above.'