The event took place at about 11.30 local time (2.30 GMT), when Kishida was preparing to make a speech after inspecting the Saigasaki fishing port in Wakayama.
Although no other details were disclosed NHK said a man was detained near the scene of the incident.
Kyodo news agency said a young man had thrown a black cylindrical object resembling a flare at the prime minister.
Japan tightened security for its authorities, following the assassination of former Prime Minister Shinzo Abe, who was the target of a deadly attack at a campaign rally in July 2022.
jrrav/mem/fvt.