The two people confirmed killed were both struck by flying debris from trees felled or uprooted by the storm.
In the Japanese capital, Tokyo, train operators delayed or cancelled services on many lines, leaving commuters stranded across the city during the busy morning rush hour.
Parts of the city also experienced power cuts.
Japan's meteorological agency warned that large parts of the country, including Tokyo, and the western industrial hub of Osaka, were at high risk of landslides as the typhoon moved along the archipelago.
Japanese car company Toyota announced that because of the typhoon it would halt production at all 12 of its domestic plants for one day.
|The storm ripped off roofs and downed power lines as it swept through Honshu [Reuters]
The typhoon had weakened slightly as it churned across Honshu, but was "still very dangerous," said Takeo Tanaka, a weather forecaster from the agency.
"Winds are violent and rain is torrential. You should also be on guard against mudslides."
Typhoon Melor was later downgraded to a tropical storm.
Melor is the latest in a series of typhoons and tropical storms to batter east Asia this year.
Japan is among the best prepared countries in the region for handling typhoons and has built extensive defences against floods and landslides, including storm surge barriers to protect coastal areas.
But despite these precautions typhoons can still cause widespread death and disruption.
In August, at least 25 people were killed when Typhoon Etau caused flash floods and landslides in Japan, even though it avoided a direct hit.
The deadliest storm to hit Japan was Typhoon Vera in 1959 which tore through Honshu, causing widespread flooding and leaving more than 5,000 dead in one of Japan's worst natural disasters.