The shrine honours millions of mostly Japanese war dead and has been criticised by countries such as China and South Korea which suffered under Japan's colonialism and aggression in the first half of the 20th century.
Tomomi Inada, Abe's hawkish new defence chief, visited Yasukuni for the first time since taking the key cabinet post in August, according to national broadcaster NHK, the Asahi Shimbun and Jiji Press.
The timing of the visit is likely to prove highly contentious coming so soon after Abe's pilgrimage with President Barack Obama to the site of Japan's December 7, 1941 attack on a US navy base in Hawaii that drew the US into World War II.
Abe and Obama paid homage to the more than 2,400 Americans killed in Japan's surprise attack against the major US naval base 75 years ago.
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They offered flowers and stood in silence before a memorial to those lost on the USS Arizona -- roughly half of all those killed in the assault.
The pair issued declarations about the power of reconciliation and warned against fomenting conflict.
Abe, a staunch conservative who has called for strengthening Japan's military, has himself avoided visiting Yasukuni in an apparent attempt to prevent controversy after going there three years ago to celebrate his first anniversary since being elected prime minister.
He has stayed away after that, but Japanese conservatives have called on him to visit the shrine again.
Dozens of conservative lawmakers visit the shrine on the anniversary marking Japan's surrender in World War II. Cabinet members also often journey to the leafy religious site during its spring and autumn festivals.
Yesterday, Masahiro Imamura, the minister in charge of the reconstruction of northern Japan after the massive 2011 tsunami, went to Yasukuni hours after Abe paid tribute in Hawaii.
Japanese media quoted him as saying the timing of his visit to the shrine was "a coincidence".
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