Japan's NHK television station said the rescued pilot had a broken leg.
An Air Force pilot was in "serious condition" Monday after a fighter jet crashed into waters south of Okinawa in southern Japan.
Japanese media reported on a second pilot that ejected from the aircraft, whose condition is also not known.
There have been several accidents involving USA aircraft as well as crimes by US servicemen on Okinawa, including rapes, fights and drunken-driving incidents.
The US has reportedly lost six aircraft since the beginning of the year in non-combat training accidents, including several fatalities.
A series of emergency landings and parts falling from United States military aircraft have highlighted safety concerns.
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A US Air Force F-15 is seen in 2009 taking off at Kadena U.S. Air Force Base on Japan's southwestern island of Okinawa.
"Your quick response proves once again how valuable an asset you are to the U.S./Japanese alliance", officials with the Kadena Air Base, the largest U.S. air base in East Asia, wrote on Twitter.
"I will ask for detailed reports about why it happened", he added.
Note that the incident occurred on June 10.
"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 base said it has "temporarily paused F-15 local training operations while the 18th Wing reviews operational, maintenance and safety procedures with unit personnel".
As Reuters additionally reported, the Japanese government is actively relocating the Futenma air base from its current location to the Henoko district of Nago city in the northern, and less populated, area of the island.