Japanese Finance Minister Taro Aso and his South Korean counterpart Choi Kyung-Hwan held a one-day meeting in Tokyo, the first since November 2012 and since conservative Prime Minister Shinzo Abe took office in December that year.
"We agreed to continue pushing for bilateral and multilateral cooperation," Aso told reporters afterwards.
In a joint statement, the ministers said that during the meeting they agreed on the importance of addressing the enormous demand for infrastructure investment in Asia. Aso said they also discussed the Asian Infrastructure Investment Bank (AIIB).
The dialogue came after a 14-year-old currency swap accord between Japan and South Korea was not renewed in February when it expired, amid soured bilateral ties.
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Relations between the two main US military allies in Asia are currently at their lowest ebb for years, dogged by issues related to Japan's 1910-45 colonial rule over the Korean peninsula and a long-running territorial row.
Choi was quoted by Jiji Press as saying: "Although there are various problems, we want to gain a chance to solve them... On the principle of separating economics from politics."