The shrine honors both Japan's war dead and war criminals convicted by an Allied tribunal.
South Korea's Yonhap News said Abe's visit Thursday would draw angry reaction from Seoul, as both China and South Korea see the Tokyo shrine as a symbol of Japan's past wartime militarism and resent Japanese leaders visiting it.
"Japan is a valued ally and friend. Nevertheless, the United States is disappointed that Japan's leadership has taken an action that will exacerbate tensions with Japan's neighbors," the U.S. Embassy in Tokyo said in a statement.
"The United States hopes that both Japan and its neighbors will find constructive ways to deal with sensitive issues from the past, to improve their relations, and to promote cooperation in advancing our shared goals of regional peace and stability," the statement continued. "We take note of the Prime Minister's expression of remorse for the past and his reaffirmation of Japan's commitment to peace."
Abe became the first Japanese prime minister to visit the shrine since Junichiro Koiuzmi did so in 2006, Kyodo News reported. During his first term as prime minister, Abe did not visit the shrine as part of an effort to improve ties with China and South Korea.
However, Abe had later described his earlier decision as regrettable. After returning to power a year ago, he expressed a desire to visit the shrine, Kyodo said.
China was quick to react to Abe's latest visit, with Foreign Ministry spokesman Qin Gang saying the visit had deeply hurt Asian war victims, the official Xinhua News Agency reported.
"We strongly protest and seriously condemn the Japanese leader's acts," Qin said.
Yonhap news said the visit would further impact Japan's already difficult relations with South Korea and China.