"Our thoughts and prayers are with our lost shipmates and their families," Rear Adm. Marc Dalton, commander, Task Force 70m, said in a statement issued on Thursday.
"As difficult as this is, we are thankful for the rapid and effective response that led to the rescue of eight of our shipmates, and I appreciate the professionalism and dedication shown by all who participated in the search efforts," said the Navy statement.
Rescuer workers rescued eight people and returned them to safety south of Japan after the US plane with 11 crew and passengers crashed into the ocean southeast of Okinawa on Wednesday afternoon.
“The aircraft was en-route to the US Navy aircraft carrier USS Ronald Reagan (CVN 76), which is currently operating in the Philippine Sea," the Navy statement said.
The military said that "personnel recovery is under way," noting "their condition will be evaluated by" the medical staff aboard USS Ronald Reagan.
The cause of the incident is not known, but according to Japanese Minister of Defense Itsunori Onodera, who said he had been informed by the US Navy, the crash may have been a result of engine trouble.
The US Navy is withholding the names of the three missing sailors pending next of kin notifications.
The plane was a C-2 Greyhound that has been in operation for more than five decades and is due to be replaced by the long-range tilt-rotor Osprey aircraft.
The aircraft carries personnel, mail and cargo from mainland bases to carriers out at sea.
Wednesday’s incident is the latest accident to hit the US armed forces in East Asia.
In August, ten US Navy personnel were killed when the USS John McCain collided with a tanker off Singapore.
Two months earlier, seven other Navy sailors were killed after the USS Fitzgerald and a cargo ship crashed into each other off Japan.
The US military has been present in the western Pacific and currently has tens of thousands of troops and hundreds of pieces of hardware stationed in Japan and South Korea.