Five people have been injured - including four seriously - in Miyazaki state, according to one local official.
"We are saying to ourselves, 'Again?'", Nobuyoshi Namikawa, a crisis management official with the Miyazaki prefectural government on Kyushu said.
Two weeks ago, three people were killed in Typhoon Man-yi, one of the most powerful typhoons to hit Japan in decades.
A fourth person remains unaccounted for.
"The typhoon isn't as big as the previous one but it's strong," Namikawa said. "We have alerted residents to be careful about gusts and rain, which can intensify suddenly as the typhoon approaches."
Ninomiya Ferry services were also suspended, public broadcaster NHK said.
About 9,700 homes in the typhoon-hit region were without power, according to the Kyushu Electric Power company.
Meanwhile, the Japan Meteorological Agency issued a tsunami warning after the Russian emergencies ministry said a series of three earthquakes killed two people on Russia's Pacific island of Sakhalin on Thursday.
The JMA registered the first earthquake with a preliminary magnitude of 6.4 off Sakhalin, but there were no immediate reports of damage or injury on Japanese territory.
Yuri Levin, acting director of the Yuzhno-Sakhalinsk seismic station, said there was no reason to panic.
"Sakhalin is in a seismically sensitive zone and there is a chance of a major earthquake sometime in the next 50 years."
Tsunami waves of about 20cm hit the coastal town of Rumoi on Japan's northernmost island of Hokkaido shortly after 1pm.