Miyazaki Airport shut its runway after the explosion caused a crater seven metres (23 feet) wide and one metre (3.2 feet) deep in the middle of the taxiway next to the runway, according to a Japanese transport ministry official.
A bomb disposal team from the Japan Ground Self-Defense Force later found that the cause of the explosion was an American bomb that had been buried beneath the land surface, probably dating to a wartime air raid, the official said.
No injuries were reported but live cam footage showed an airplane had been taxiing nearby just two minutes before the explosion, according to local broadcaster MRT.
The runway shutdown has led to the grounding of 87 flights but there is no danger of any further explosions and repair works to fill the hole should be completed by Thursday morning, said Japan's top government spokesperson Yoshimasa Hayashi.
The affected flights were operated by JAL, ANA and other airlines connecting Miyazaki with cities such as Tokyo, Osaka and Fukuoka, according to the airport website.
Located at the southeast end of Kyushu island, Miyazaki airport was formerly a Japanese navy base until the end of World War Two, from where hundreds of young "kamikaze" pilots set off on their final missions, according to the Miyazaki city website.
Multiple unexploded bombs have previously been found at Miyazaki airport, the transport ministry official said.
More than 79 years since the end of the war, unexploded bombs from the intense airstrikes are still found across Japan today. A total of 2,348 bombs weighing 37.5 tonnes were disposed of during fiscal year 2023, the Self-Defense Forces have said.