The figure, provided by police, includes people whose deaths are suspected to be linked to the disaster, public broadcaster NHK quoted a government spokesman in Tokyo as saying.
Authorities in Kumamoto prefecture on Japan's south-western main island earlier reported 17 confirmed deaths, according to the Kyodo news agency.
Search and rescue operations were continuing after the magnitude-7.1 earthquake struck on Tuesday afternoon.
Many buildings in the region were destroyed, raising fears that the death toll could rise further. Dozens of people were also injured, according to local media.
More than a day after the powerful quake, thousands of households remained without electricity or running water.
More than 10,000 people were still staying in emergency shelters early on Thursday.