"Both of these countries are strong, important, valued allies of the United States. It's obviously not comfortable for us when they have a dispute between them," State Department spokeswoman Victoria Nuland told reporters.
"So our message to each of them is the same: Work this out, work it out peacefully, work it out through consultations," she said.
The two nations had worked in recent years to repair relations. But many Koreans remain bitter over Japan's 1910-1945 occupation, and tensions flared on August 10 when South Korean President Lee Myung-Bak paid an unprecedented visit to disputed islands.
In an increasingly bitter tit-for-tat, South Korea refused to accept delivery of a protest note by Japanese Prime Minister Yoshihiko Noda.
Tokyo accused its neighbour of breaching diplomatic norms and refused to take the letter back.
The United States has tried to stay studiously neutral on the emotive dispute, although both sides have sought Washington's validation of their claim to the Seoul-controlled islands known as Dokdo in Korea and Takeshima in Japan.
Nuland said that senior Japanese diplomat Shinsuke Sugiyama raised the issue when he met Wednesday in Washington with Kurt Campbell, the assistant secretary of state handling East Asia.
"My understanding is that the Japanese side brought it up and that our side said what we always say, publicly and privately - that we want to see the two countries work it out together," Nuland said.
Sugiyama also met other US officials including Glyn Davies, the US pointman on North Korea.
US analysts have voiced concern that the flare-up between its northeastern Asian allies have set back broader interests in the region, where concerns remain high over North Korea and China is rising in clout.
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