"Our hearts and prayers go to the pilot and his family as they go through this hard time", Kadena Air Base' official Twitter account said.
Takeshi Onaga, governor for Okinawa, has called on the USA military to suspend flights of F-15 jets until the aircraft are declared safe.
The condition of the rescued pilot, who ejected, was not immediately known, the sources added.
The U.S. military has launched an investigation into the crash.
The U.S. military says an Air Force F-15C fighter jet has crashed in waters south of Okinawa in southern Japan. The lone pilot "successfully ejected" and was rescued by Japan Air Self-Defense Force, but remains in serious condition after being transferred to the U.S. Naval Hospital, Kadena officials said.
Kadena is the largest U.S. military base in Japan, which hosts around 47,000 American troops under a decades-long security alliance.
The incident marks the 12th crash involving USA military aircraft this fiscal year.
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Calling for a detailed report into the latest incident, Itsunori Onodera, Japan's defence minister, told Kyodo news agency: "Accidents of United States military aircraft are occurring repeatedly".
"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.
"We can not fulfil our responsibilities to our children and their children if such a situation becomes the norm", Okinawa governor Takeshi Onaga said.
The Okinawa government asked the U.S. military to suspend F-15 flights until they are confirmed safe, while the prefectural government and local towns hosting the base are set to lodge protests against the USA military. "I don't think there is a country like this among developed nations".
The Okinawa island houses more than 70% of all U.S. military facilities in Japan.
F-15 fighter jets are twin-engined tactical fighters that were initially envisioned as a pure air superiority vehicle.