The C2-A Greyhound transport plane was carrying 11 crew and passengers to an aircraft carrier when it crashed into the Philippine Sea around 2:45 p.m. Japan Standard Time, the Navy said.
Eight people have been rescued and are in good condition aboard the carrier, the USS Ronald Reagan, the Navy said in a statement
. US and Japanese ships and planes are searching the area for the three people who remain missing.
The names of those who were onboard are being withheld, pending the notification of their next of kin, the Navy said.
"Our entire focus is on finding all of our sailors," Navy Rear Adm. Marc H. Dalton said. "US and Japanese ships and aircraft are searching the area of the crash, and we will be relentless in our efforts."
The search for the aircraft's crew members was expanded. By Thursday morning, US and Japanese forces had covered more than 320 nautical miles, the Navy said.
The plane 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 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.
The cause of the crash wasn't immediately known, according to an initial statement from the US Navy 7th Fleet.
"I have been informed from the US military that engine trouble may have caused (the crash)," Japan's Defense Minister Itsunori Onodera told reporters Wednesday.
Troubled year for Navy in Pacific
It's been a difficult year for the Navy in the western North Pacific following a spate of incidents -- most involving ships assigned to the East Asia-based US 7th fleet -- that included the deaths of 17 sailors.
In August, Vice Adm. Joseph Aucoin was relieved of his duty
as the commander of 7th Fleet following a deadly collision between the destroyer USS John S. McCain and a merchant ship off Singapore
that left 10 US sailors dead.
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.
On Saturday, a Japanese tugboat lost propulsion and drifted into the USS Benfold
in a bay off central Japan, causing minor damage to the guided-missile destroyer, the Navy said.
Another incident in East Asian waters involved a US 3rd Fleet ship:
In May, the guided-missile cruiser USS Lake Champlain was struck by a South Korean fishing boat
off the Korean Peninsula.
The Navy has launched multiple investigations and reviews in the wake of this year's accidents.
The C2-A that crashed Wednesday belongs to a Japan-based squadron that generally flies cargo and passengers
between shore bases and the USS Ronald Reagan.