Masahiro Imamura, the minister in charge of the reconstruction of northern Japan after the massive 2011 tsunami, visited Yasukuni Shrine in the afternoon, his secretary said.
The secretary could only confirm the visit but had no information on why Imamura chose to visit at this time.
"I reported about work to the gods and prayed for our country's peace and prosperity," he said, according to the Asahi Shimbun daily.
"I decided about a week ago to visit the shrine," Imamura added, stressing it "has nothing to do with" Abe's trip to Pearl Harbor.
The shrine has for decades been a flashpoint for criticism by countries such as China and South Korea that suffered under Japan's colonialism and aggression in the first half of the 20th century.
The indigenous Shinto religious shrine honours millions of mostly Japanese war dead, as well as senior military and political figures convicted of war crimes after the war.
Imamura's visit came just hours after Abe and US President Barack Obama paid homage to the more than 2,400 Americans killed on December 7, 1941 in Japan's surprise attack that drew the United States into World War II.
The pair issued declarations about the power of reconciliation and warned against fomenting conflict.
Abe, a staunch conservative who has called for beefing up Japan's military, himself has avoiding visiting Yasukuni in an apparent bid to prevent controversy after going there three years ago on Monday.
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