The plane took off on a routine training mission.
A U.S. F-15 fighter jet, the same type that crashed into the sea south of Naha, Okinawa Prefecture, on June 11, 2018.
Japanese coast guard and self-defence forces responded to the incident, reportedly dispatching an urgent rescue team to the crash site.
The U.S. military has launched an investigation into the crash.
The minister added he hopes to obtain a detailed report on the cause of the latest crash as Japan also uses the F-15.
The Kyodo news agency said the jet belonged to the US Kadena Air Base and crashed early Monday morning about 80 kilometres south of Naha, the regional capital of Japan's southern Okinawa island. The southernmost island prefecture hosts the bulk of United States military facilities in Japan.
"I want to firmly demand safe flights", he said adding that he has asked the US military to implement safety management thoroughly and take measures to prevent a recurrence.
Many Okinawa residents blame the USA bases for crime, accidents and pollution and want them moved off the island, the Reuters news agency points out, adding that, "A series of emergency landings and parts falling from us military aircraft have highlighted safety concerns".
"If that happens, we can not fulfill our responsibilities to our children and grandchildren", Onaga said.
In March, Japanese officials called on the USA military to provide information after an antenna fell from an Okinawa-based F-15 on February 27.
A U.S. F-15 jet fighter leaves after an airstrike against Taliban insurgent positions in eastern Afghanistan's Kunar province, near the border with Pakistan, Aug. 28, 2011.