The Kumamoto disaster management office issued the new tally for Tuesday's quake, with seven bodies now extracted from the mass of rubble, steel and wires of the Aeon shopping mall after a suspected gas blast.
Eight people were also confirmed dead at the Nippon Paper Industries factory in Yatsushiro city, where part of a red-and-white smokestack collapsed, according to the office.
Five others were in a critical condition after the 7.1-magnitude tremor, while almost 9,500 locals were in evacuation centers in the region of southwestern Japan on the island of Kyushu.
The quake caused widespread damage, flattening homes, damaging bridges, triggering fires and leaving tens of thousands of residents without power and water in temperatures forecast to hit 38C this weekend.
Some 13,520 households remained without electricity on Thursday.
