Chief Cabinet Secretary, Yoshihide Suga,said he doubted whether Ban was fully aware of the efforts Japan was making towards dialogue with China and South Korea, amid disputes over territory and historical differences.
Suga added that Tokyo would ask Ban, a former South Korean Foreign Minister, to explain what he meant when he urged Japanese leaders to conduct "very deep introspection".
"Prime Minister (Shinzo Abe) has called for dialogue with South Korea and China despite issues of concern," Suga told a regular press briefing.
Tokyo's relations with its neighbours have been regularly strained by the legacy of Japan's wartime aggression, as well as territorial disagreements.
Shinzo Abe, who came to power in December, has not yet held summit talks with his counterparts in China and South Korea.
Speaking in Seoul yesterday, Ban called for "very deep introspection" by Japanese leaders, especially with regard to moves in Japan to revise its pacifist constitution.
"I find it very regrettable that the tension (among the three northeast Asian countries) continues on due to issues of history and other political reasons," Ban told reporters.
Calls from Seoul and Beijing for Japan to "correctly" view its past deeds are common, as is the claim from all sides that the other side does not "understand" its position and actions.
Abe has been opaque about whether he believed in Japan's apologies to Asian nations about harm caused to them before and during World War II.
But the premier has largely kept away from issues relating to history since coming to power and focused his political capital on boosting Japan's ailing economy.
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