The unapologetically nationalist Abe donated a sacred "masakaki" tree to coincide with the start of a three-day festival, a shrine official said, two days ahead of the arrival of US President Barack Obama.
The sending of a gift has been seen as a sign that Abe does not intend to visit, as he did on Dec 26, sparking fury in Asia and earning him a diplomatic slap on the wrist from the United States, which said it was "disappointed".
That, and the accompanying museum -- which paints Japan as a frustrated liberator of Asia and victim of WWII -- makes it controversial, especially in China and South Korea, where it is seen as a symbol of Japan's lack of penitence.
Abe and other nationalists say the shrine is merely a place to remember fallen soldiers. They compare it with Arlington National Cemetery in the United States.
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Masaru Ikei, an expert on Japanese diplomacy and professor emeritus at Keio University, said with Obama due to arrive on Wednesday for a state visit, Abe was always likely to stay away.
Ikei said Washington's very public and slightly unexpected rebuke after his last visit meant Abe "will not be able to visit the shrine again for a while".
Japan's chief government spokesman Yoshihide Suga today sought to play down Abe's shrine gift.
"I'm aware that the prime minister offered Masakaki (sacred tree)," he told reporters.
"The offering was made in his capacity as a private person, and so the government should not comment on such an act by him."
Many conservative lawmakers are expected to go to the shrine to mark the spring festival on tomorrow.
Two of Abe's cabinet ministers have already visited, saying they did not want the visits to interrupt their official duties.