The "masakaki" tree offering by Abe comes on the first day of the shrine's two-day spring festival and was made in the name of the prime minister.
The Japanese leader, however, did not visit the controversial shrine in person.
The Shinto shrine, seen by neighboring countries as a symbol of Japan's past militarism, has long-been a source of diplomatic friction with Japan's neighbors as it honors convicted war criminals together with the war dead.
Yasukuni Shrine honors 14 Class-A convicted war criminals among 2.5 million Japanese war dead from World War II (WWII) and is regarded as a symbol of Japan's past militarism.
Visits and ritual offerings made in person or by proxy to the infamous shrine by Japanese leaders and officials have consistently sparked strong criticism and hurt the feelings of China and South Korea and other countries brutalized by Japan during WWII.
Abe has sent a ritual offering to Yasukuni during the shrine's spring and autumn festivals every year since he launched his current administration in 2012.
The Japanese prime minister last visited the controversial shrine in person in December 2013, at which time he was strongly condemned by China and South Korea, as well as the United States, who said at the time it was disappointed with Abe's decision.
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