Chief Cabinet Secretary Yoshihide Suga, the government's chief spokesman, told reporters that UNESCO's decision reflected only China's views over the 1937 assault on the Chinese city, when Japanese troops massacred between 40,000 and 300,000 Chinese civilians in what has become known as the Nanjing Massacre.
Chinese and Japanese estimates vary regarding how many people died in the massacre, viewed as one of the worst atrocities of the World War II era.
"The decision making process lacked transparency," he said. "We were not even allowed access to the contents of the Chinese documents."
According to the Japanese Foreign Ministry, Japan contributed 3.72 billion yen (about USD 31 million) to UNESCO in 2014, or 10.8 per cent of its budget assessed for the UN.
UNESCO's budget for the two-year 2014-2015 period is USD 653 million. Japan has also set up various trust funds to support work on world and cultural heritage efforts.
While Japan objected to the inclusion of the documents on the Nanjing Massacre, it succeeded in having some of its own candidates for the memory list included, including details on detainees held in Siberia after World War II.
Materials submitted by China for inclusion in the Memory of the World Register in 2014 included documents about the period of the massacre, about the postwar investigation and trials of war criminals documented by the Chinese National Government's Military Tribunal in 1945-47 and 1952-56 files from China's judiciary.
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