The leafy "masakaki" plant was sent for the shrine's spring festival the same day that more than 90 Japanese lawmakers and Internal Affairs Minister Sanae Takaichi visited Yasukuni.
Abe has made regular offerings for Yasukuni's seasonal festivals but has not visited the shrine since December 2013, when he drew rebukes not only from China and South Korea but also the United States.
As victims of Japan's aggression before and during World War II, China and South Korea see the shrine as a symbol of Japan's militarism.
In Beijing, Foreign Affairs Ministry spokesman Lu Kang said "the ones who attended the Yasukuni shrine are honouring war criminals who have direct responsibility for crimes committed during World War II."
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He urged Japan to "reflect and examine their history of colonisation, and to sever ties with their militarism past."
Chief Cabinet Secretary Yoshihide Suga said Abe's offering was made in a "personal capacity," but declined to comment further.