Earlier in the day, Suga sent a "masakaki" tree to the controversial Yasukuni Shrine in Tokyo in line with an annual autumn festival.
It marked the first time that Suga sent such an offering to the war shrine since he took office in September. He succeeded his predecessor Shinzo Abe, who resigned due to health issues.
"We express deep regrets that Japanese government and parliamentary leaders sent offerings again to the Yasukuni Shrine that glorifies Japan's history of wars of invasion and honors war criminals," Seoul's foreign ministry said in a statement.
"Our government strongly called on responsible Japanese leaders to respond to calls for the future-oriented development of South Korea-Japan relations by facing history squarely and humbly reflecting on and genuinely atoning for past history through actions on the occasion of the launch of the new Cabinet," it added.
Yasukuni Shrine honors Japan's war dead, including 14 Class A war criminals. Visits to the shrine by Japanese leaders have been a key source of tension in the region as Asian neighbors view the visits as an attempt to beautify the country's militaristic past.
Abe visited the shrine last month for the first time in nearly seven years. He had not visited Yasukuni as prime minister since his last visit in 2013 sparked criticism from South Korea and China, which suffered Japanese aggression in the 20th century.
Meanwhile, South Korea's new coronavirus cases rebounded above 50 on Saturday on cluster infections, putting health authorities on alert over a potential uptick in daily infections amid eased virus curbs.
The country added 73 more Covid-19 cases, including 62 domestic infections, raising the total caseload to 25,108, according to the Korea Disease Control and Prevention Agency (KDCA).
It marked a rise from 47 daily cases Friday but a decline from 110 cases Thursday, when more than 50 reported cases were tied to a nursing home in the southern port city of Busan.
New virus cases dropped below the 50 mark for the first time since Sept. 29 on Friday, but health authorities remain vigilant about a potential spike in sporadic cluster infections.
On Monday, the country relaxed its tougher virus curbs by one notch to the Level 1 social distancing measures in its three-tier scheme as new virus cases slowed down after a resurgence.
Daily infections had been in the triple digits for more than a month since Aug. 14. New virus cases have largely slowed down on the back of weekslong stricter virus curbs put in place in late August. (Yonhap-The Korea Herald/Asian News Network)
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