The Yasukuni shrine in Tokyo honours some 2.5 million war dead, mostly Japanese, who perished in the country’s wars since the late 19th century.
But it also honours senior military and political figures convicted of war crimes, and has frequently been a source of sour relations with countries that suffered from Japan’s military atrocities, particularly China and South Korea.
Suga’s predecessor Shinzo Abe, who stepped down last year for health reasons, visited the shrine in person as it marks a spring festival, a Yasukuni spokeswoman said.
Suga sent a sacred tree to mark the spring festival but was not expected to visit the shrine in central Tokyo.
A 2013 visit to the shrine by Abe, when he was serving as prime minister, sparked outcry from Beijing and Seoul, as well as a rare diplomatic rebuke from close ally the United States.