The Japan Meteorological Agency downgraded the special warnings for heavy rains, issued on Monday for northern parts of the island, to lower-level warnings and advisories, but urged residents to stay alert for further landslides.
Japan is the latest country to be hit by unusually heavy rain in various parts of the world in recent days that has raised new fears of the pace of climate change.
"Municipalities are still making checks on casualties, ... but we were informed of three deaths, another three deaths potentially related to the disaster, three missing and two lightly injured," Chief Cabinet Secretary Hirokazu Matsuno told a regular news conference.
The rain forced tire maker Bridgestone to suspend operations at four factories on Kyushu on Monday, but the plants resumed operation by Tuesday morning, a company spokesperson said.