"The application is trying to embellish the invasion history of Japanese militarism and challenge the achievements of the world anti-Fascism war and post-war international order," Foreign Ministry spokeswoman Hua Chunying told a media briefing answering a question.
The application was made by the Chiran Peace Museum in Minamikyushu city.
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Hua said Japan committed many atrocities against humanity during World War II.
The kamikaze were suicide pilots recruited by Japan to attack Allied naval vessels during the closing stages of the Pacific campaign of World War II. Their attacks were designed to run down warships more effectively than conventional attacks.
Although numbers quoted vary, at least 300 Allied vessels were damaged. The kamikaze also caused serious losses to the American Pacific fleet, especially at Okinawa.
"The application is completely against the mission of the UNESCO to maintain world peace and will surely be strongly condemned and firmly opposed by the international community," Hua said.
The 333 notes and letters are part of 14,000 pieces of writing kept in the museum, state-run Xinhua news agency reported.