Japanese Prime Minister Shinzo Abe did not personally visit the Yasukuni Shrine on Thursday, the first day of an annual autumn festival, but did send a ritual offering. Many see Yasukuni as a symbol of Tokyo's imperialist past.
China and South Korea, both victims of Japanese war-time aggression, regularly complain when Japanese leaders visit the Tokyo memorial.
Yasukuni honors Japan's nearly 2.5 million war dead, including 14 convicted war criminals from WWII.
This is the third time Abe has sent an offering to the shrine since becoming prime minister in December.
Deputy Chief Cabinet Secretary Katsunobu Kato said it is not the government's place to comment on such "personal acts," but said he understood the sentiment being expressed.
"Praying for those who have given their lives to protect their country from threats both inside and out and paying one's respects is only natural," said Kato.
A shrine official confirmed that Abe's offering was received, noting that it was made in the name of the prime minister.
There has been no response from China or South Korea yet, which have recently accused Japan of not showing proper remorse for its past.
China-Japan ties have also been damaged by a recent flare-up in a territorial dispute over a group of uninhabited islands in the East China Sea.