Beijing and Seoul have both refused to meet with conservative Prime Minister Shinzo Abe, citing what they say is his lack of remorse for World War II wrongs and his intention to remilitarise Japan.
"Individual problems that we have with China and South Korea are the kind of issues that are difficult to solve in the short term," Kishida said.
"But I wonder if it's right to take the attitude that we should not have talks because we have issues.
Abe, China's President Xi Jinping and South Korean President Park Geun-Hye all came to power around a year ago, but entrenched positions and growing nationalism in the three countries has prevented them from getting together.
Seoul and Beijing were angered by Abe's visit last month to a shrine in Tokyo that counts 14 senior war criminals among the 2.5 million souls it commemorates.
China and South Korea see the shrine as a symbol of Japan's wartime aggression in Asia.
Abe defended the visit as a pledge against war and said it was not aimed at hurting feelings in China and South Korea.
The diplomatic scrap between Tokyo and Beijing has increasingly spilled out onto the world stage, with dozens of Chinese diplomats penning op-ed pieces in newspapers around the world seeking to swing global public opinion behind them.
China's envoy to the African Union this week launched an attack on Abe in a press conference, warning of the impending "resurrection of Japanese militarism" and branding the premier a "troublemaker".
Tokyo launched its latest rebuttal today, with the publication in the Washington Post of an opinion piece by Kenichiro Sasae, its ambassador to the US, in which he said Beijing's "anachronistic propaganda" was out of step with the world.
"China has quadrupled its military expenditures, which are hardly transparent, in the past decade. During the same period, Japan has decreased its expenditures by 6 per cent," he wrote.
The row over uninhabited islands in the East China Sea continues to draw significant attention in foreign policy circles, with some observers warning of the danger of an armed clash and others drawing comparisons with Sarajevo in 1914, when a localised act of violence flung an entire continent into war.
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