U.S. Secretary of State John Kerry and Defense Secretary Chuck Hagel visited the secular Chidorigafuchi National Cemetery in Tokyo but gave the religious Yasukuni Shrine a wide berth.
The cemetery houses the remains of more than 350,000 unidentified war dead from World War II, while Yasukuni honors convicted World War II criminals among the war dead.
Kyodo News reported that Kerry and Hagel were the highest-ranking U.S. officials to visit the cemetery.
The visit is seen as an attempt by Washington to bolster the alliance with Tokyo while avoiding being associated with the Abe administration's lurch to the chauvinist far right.
The Chidorigafuchi National Cemetery was created in 1959 and liberal Japanese have called on Japanese politicians to visit that rather than Yasukuni.
In a piece for the U.S. magazine Foreign Affairs in May of this year, Japanese Prime Minister Shinzo Abe raised eyebrows by likening visits to Yasukuni to paying homage to American war dead at the Arlington National Cemetery near Washington.
Abe did not visit Yasukuni on Aug. 15, which marks the end of World War II, and sent an offering instead, but a record number of government officials and lawmakers paid their respects at the shrine.