The comments came after Chinese President Xi Jinping and his South Korean opposite number Park Geun-Hye, during summit talks yesterday, reportedly discussed joining forces for the 70th anniversary next year of Japan's defeat in World War II.
At a regular press conference in Tokyo, Chief Cabinet Secretary Yoshihide Suga said such moves were divisive.
"Any attempt by China and South Korea to coordinate in picking apart past history unnecessarily and making it an international issue is utterly unhelpful for building peace and cooperation in the region," he told reporters.
"Japan believes that such issues should not be treated as diplomatic issues," Japanese Foreign Minister Fumio Kishida told reporters in Tokyo after suggestions Beijing and Seoul could also co-ordinate research into wartime sex slavery.
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Around 200,000 women, mainly from Korea but also from China, Taiwan and Indonesia among others, were forced to work in brothels as "comfort women", serving imperial troops as Japan stomped across Asia before and during World War II.
This equivocation irritates Seoul, which sees it as symptom of Japan's lack of penitence.
The China-South Korean summit came after Beijing began publishing what it said were the "confessions" of 45 convicted Japanese war criminals.
China regularly accuses Japan of failing to face up to its history of aggression in Asia, criticism that has intensified under Abe, who won elections in December 2012 and has advocated a more muscular defence and foreign policy stance.
Both countries have also expressed disquiet over Japan's decision this week to expand the scope of its military, allowing for the first time troops to fight on behalf of an ally under attack.