"Our thoughts and prayers are with our lost shipmates and their families," said Rear Adm. Marc Dalton, commander, Task Force 70. "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, which was released Thursday.
The Navy is withholding the names of the three sailors pending next of kin notifications.
The sailors were aboard a C2-A Greyhound transport plane that crashed into the ocean southeast of Okinawa on Wednesday afternoon.
A total of 11 crew and passengers were headed to an aircraft carrier when the plane crashed into the Philippine Sea around 2:45 p.m. Japan Standard Time, the Navy said.
Seven US Navy and Japan Maritime Self-Defense Force ships, three helicopter squadrons and maritime patrol aircraft covered nearly 1,000 square nautical miles in the search.
The aircraft was carrying passengers and cargo from Marine Corps Air Station Iwakuni in Japan to the carrier when the plane crashed about 500 nautical miles southeast of Okinawa, Japan.
A C-2A Greyhound plane launches from the USS Ronald Reagan during a 2017 exercise.
A Navy public affairs officer told CNN the plane was on approach to the carrier, but didn't know how far away it was from the ship.
Troubled year for Navy in Pacific
It's been a difficult year for the Navy in the western North Pacific after a spate of incidents -- most involving ships assigned to the East Asia-based US 7th fleet -- that included the deaths of 17 sailors.
Those two fatal collisions were "avoidable" and "numerous failures occurred on the part of leadership," a Navy report concluded earlier this month.
At least two other incidents involving US 7th Fleet ships happened in waters off East Asia this year.
The Navy has launched multiple investigations and reviews in the wake of this year's accidents.
CNN's Ivan Watson, Junko Ogura, Emily Smith and Rebecca Wright