Prime Minister Prayut Cha-o-cha handed over the donation to the Japanese ambassador to Thailand, Shiro Sadoshima, at Government House on Monday as a show of support and sympathy from the Thai government.
Devastating floods and landslides have struck the western part of Japan since July 5 following prolonged torrential rain.
The death toll reached 210, with 22 still unaccounted for, including 4,800 who are still staying at evacuation shelters in 14 prefectures.
About 162,000 households are still getting by without running water