An unsuccessful bid last year by the city, which hosted an airfield from which hundreds of pilots launched suicide missions 70 years ago, was condemned by China, where memories of Japan's occupation run deep.
Both China and Korea suffered under Japanese rule, with parts of China occupied in the 1930s and Korea colonized from 1910 to 1945.
"Our project is in no way whatsoever being undertaken in an attempt to glorify, romanticize or otherwise rationalize the historical legacy of (the pilots)," Shimoide told a news conference, referring to the letters and wills from the pilots preserved at the Chiran Peace Museum.
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China applied last year for the inclusion of documents from the 1937 Nanjing Massacre and archives about the women forced to work in wartime Japanese military brothels under the same programme, prompting protests from Japan. A decision on this is expected later this year.
The Minamikyushu bid failed to clear the Japanese domestic selection process last year. Should it succeed this time, it would be considered for listing in 2017.
UNESCO's Memory of the World programme, launched in the 1990s, has registered dozens of projects to reflect the "documentary heritage" of different periods. Documents include Britain's 13th century Magna Carta, Anne Frank's diary from World War Two and an annotated copy of Karl Marx's Das Kapital.
"This project is being undertaken to make a contribution to lasting peace in humanity's future," said Mordecai George Sheftall, a historian and professor at Shizuoka University in Japan. "The world needs the Chiran documents so that nothing like the kamikaze will happen again." (Reporting by Kiyoshi Takenaka, Writing by Elaine Lies; Editing by Nick Macfie)
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