No Japanese premier has visited Yasukuni Shrine since 2013 and Ishiba's predecessor Fumio Kishida would also regularly send offerings for its biannual spring and autumn festivals.
Yasukuni in central Tokyo is dedicated to 2.5 million war dead, mostly Japanese, who have perished in conflicts since the late 19th century.
But this includes senior military and political figures convicted by an international tribunal of war crimes prior to and during World War II.
Every year, dozens of lawmakers pay their respects during the spring and autumn festival and in August for the anniversary of the emperor announcing Japan's surrender in 1945.
But a Japanese prime minister has not appeared there since 2013, when Shinzo Abe sparked fury in Beijing and Seoul and earned a rare diplomatic rebuke from close ally the United States.
The minister of health, labour and welfare, Takamaro Fukuoka, also sent a "masakaki" tree offering, the spokesman for the shrine told AFP.
Seoul expressed "deep disappointment and regret that responsible leaders in Japan have once again offered tribute or visited the Yasukuni Shrine," South Korea's foreign ministry said Thursday.
"We urge the leaders of the new Japanese cabinet to squarely face history and show through action humble reflection and genuine atonement for past wrongdoings."
When asked about the matter at a regular briefing, Beijing's foreign ministry spokeswoman Mao Ning called Yasukuni "a symbol of Japan's militaristic war of aggression".
"We urge Japan to face up to and reflect on its history of aggression (and) to be cautious in words and deeds regarding historical issues such as Yasukuni Shrine," she said.
That will help Japan "gain the trust of Asian neighbours and the international community through concrete actions", Mao added.
