Kishida sent a "masakaki" tree to the Yasukuni Shrine in Tokyo earlier in the day to celebrate its two-day autumn festival that runs through Monday, according to Japan's Kyodo news agency and South Korean Foreign Ministry officials.
It marked the first time Kishida has sent an offering to the shrine, seen as a symbol of the country's past militarism, since he took office earlier this month.
Kishida stopped short of visiting in person, but his predecessor, Yoshihide Suga, visited the shrine earlier in the day, they added.
"The government expresses deep disappointment and regrets that Japanese leaders again sent the offering or repeated their visits to the Yasukuni Shrine," Yonhap News Agency quoted Seoul's Foreign Ministry as saying in a statement.
The Yasukuni Shrine honours 2.5 million Japanese war dead, including 14 Class-A criminals from World War II.
Visits to the shrine by Japanese leaders have long been a key source of tension in the region as Asian neighbours, like South Korea and China that suffered from Japanese aggression in the early part of the 20th century, view the visits as an attempt to beautify the country's militaristic past.
South Korea also pressed Japanese leaders to "squarely face history and show by action their humble introspection on and genuine self-reflection for the past history".
South Korea and Japan are close economic partners and key allies of the US, though they have long been in conflict over territory and other historical disputes stemming from Japan's colonial rule of the Korean Peninsula from 1910-45.
On Friday, South Korean President Moon Jae-in and Kishida held their first phone call and agreed to accelerate the bilateral diplomatic consultations to resolve a prolonged feud over wartime forced labour and to develop their ties "in a future-oriented manner".