Japan’s last outbreak of bird flu was in January 2018, also in Kagawa prefecture, when 91,000 chickens were culled.
Helicopters and boats have rescued more people from their homes in the Kumamoto region. More than 40,000 defense troops, the coast guard and fire brigades have been taking part in the operation.
About 900 mm of rain has fallen on the southernmost main island of Kyushu since late June, with heavy rain forecast to continue into Thursday.
Officials put the toll at 48 with 28 others presumed dead after unprecedented rain forced several million people from their homes, media reports say, with more rain set to hit some areas for at least another day.
Japanese Prime Minister Shinzo Abe cuts short a European tour and visits the flood-hit southwestern island of Kyushu, promising his government's support.
Several thousand people have been evacuated from their homes due to the flooding exacerbated by Typhoon Nanmadol. Rescue operations are continuing and the death toll may rise.
The season's third typhoon made landfall in Nagasaki prefecture. At least three people have been injured and up to 47 domestic flights were cancelled.
Death toll reaches 48 from two powerful earthquakes in Japan
Magnitude 6 quake in southern Japan kills nine and injures hundreds after bringing down buildings
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