Defence Minister Minoru Kihara, Economic Security Minister Sanae Takaichi, and Yoshitaka Shindo, the economic revitalisation chief, visited the site in Tokyo on Thursday.
Fourteen prominent convicted war criminals, including wartime prime minister Hideki Tojo, are among the 2.5 million war dead honoured at the shrine.
"I would like to express my heartfelt condolences today to all those who sacrificed their precious lives and pay my deepest respect," Kihara said at the shrine, in comments aired on television.
The visits are the first by senior government officials since Japanese Prime Minister Fumio Kishida and South Korean President Yoon Suk-yeol agreed with US President Joe Biden to pursue deeper security ties.
Minister Minoru Kihara offered his "heartfelt condolences" while visiting the Yasukuni shrine. (AP PHOTO)
"I understand that all of them visited the shrine in their private capacity and that it is not a matter for the government to comment on," Japan's top government spokesperson, Yoshimasa Hayashi, told a news conference.
"It is natural for any nation to pay respect to those who have given their lives for their country."
South Korea, a Japanese colony for 35 years, and China, which was invaded by Japan, see the shrine as a magnet for conservatives who want to gloss over their neighbour's wartime actions.
"Our government urges responsible Japanese leaders to face history and demonstrate humble reflection and genuine introspection," South Korea's foreign ministry said.
"This is an important foundation for the development of forward-looking relations."
China had made serious representations to the Japanese side and had made its position clear, its foreign ministry said.
Supporters of Yasukuni, established in 1869 as Japan emerged from more than two centuries of isolation, say it commemorates all the war dead and not only those blamed for waging war on neighbours.
"We can live happily now because our ancestors fought in the war," said Yuka Watanabe, 50, a visitor to the shrine, where men wearing World War II-era military uniforms bowed and marched with flags.
"I don't think we should ever forget that."
Kishida, who plans to step down in September, stayed away, sending an offering instead.
Takaichi is among about half-a-dozen people touted as his possible successor.
No serving Japanese prime minister has visited Yasukuni, which means "peaceful country" in Japanese, since Shinzo Abe in 2013, a visit that prompted an expression of disappointment by then-US president Barrack Obama.
