Earlier, Kishida toured the town of Bucha, where the mayor has said more than 400 civilians were killed last year by Russian forces and which has since become synonymous with Russian brutality during the war.
He laid a wreath outside a church before observing a moment of silence and bowing.
“The world was astonished to see innocent civilians in Bucha killed one year ago. I really feel great anger at the atrocity upon visiting that very place here,” Kishida said.
“I would like to give condolence to the all victims and the wounded on behalf of the Japanese nationals. Japan will keep aiding Ukraine with the greatest effort to regain peace.”
Kishida’s trip coincides with Chinese President Xi Jinping’s state visit to Russia. In what appeared to be a response to Kishida’s trip, Russia’s defence ministry said on Tuesday that two of its strategic bomber planes flew over the Sea of Japan for more than seven hours.
Japan is due to host a G7 summit in Kishida’s hometown of Hiroshima in May. Tokyo has continually voiced support for Ukraine and joined rounds of sanctions against Russia.
His trip was kept secret until the last minute for security reasons. It is rare for a Japanese leader to make an unannounced visit to another country.
Public broadcaster NHK showed footage of Kishida talking to officials after his arrival in Kyiv by train, which he had taken from the Polish border town of Przemysl.
Kishida has said that the G7 summit should demonstrate a strong will to uphold international order and rule of law in response to the Ukraine war.
Japan, a key ally of the United States, has its own territorial dispute with Moscow that dates back to the end of World War Two. Russia’s invasion has also deepened concern in Tokyo and among the Japanese public about what would happen to Japan if China were to invade Taiwan.
Encouraged by the United States, Japan in December unveiled its biggest military build-up since World War Two, with a commitment to double defence spending to 2% of gross domestic product within five years.
Kishida will also meet his Polish counterpart before returning to Japan on Thursday, the ministry said.
Prior to leaving for Poland en route to Ukraine, Kishida visited India, where he met Prime Minister Narendra Modi.