Japanese Transport Minister Tetsuo Saito told a briefing on Friday that he had "ordered the magnetic search at Miyazaki airport" and other airports.
The search will initially focus on airports in the regional commercial hubs of Sendai, Fukuoka and Naha, according to national broadcaster NHK.
All once hosted wartime military facilities, local media said.
At Miyazaki, three bombs have been found since 2011, including a one-tonne device discovered during resurfacing work at the airport's parking apron.
Miyazaki airport originated in 1943 as an imperial Japanese navy base, sending dozens of "kamikaze" aircraft on suicide missions.
Before the nuclear bombings of Nagasaki and Hiroshima in 1945, the US Air Force heavily bombarded dozens of Japanese cities.
In the year to April 2024, Japan's military safely removed 2,348 unexploded devices, 441 of them in the southern region of Okinawa, according to the Self Defence Forces. (AFP)