The EA-6B Prowler went down about 10 miles outside of Harrington, Wash. just before 9 a.m.
The Navy informed Congress that the wingman of the crashed plane reported that no parachutes were deployed.
"First responders are on the scene and have reported finding partial remains of the mishap aircrew," the Navy informed Congress.
The identities of the crew were not immediately available.
The Prowler was "engaged in a low-level navigation training mission," the Navy told Congress. Whidbey Island officials said the cause of the accident was under investigation.
NAS Whidbey Island is home to the U.S. Navy's tactical electronic warfare squadrons. Crews from the base, located on Puget Sound, regularly fly across Eastern Washington for training exercises.
HaLee Walter lives nearby and said she heard a huge explosion that shook her house when the plane crashed.
"I went outside and of course I could see the smoke," she said. "The ambulance and police and fire trucks were all there and a plane had gone down and there was still another military aircraft circling."
Stan Dammel, who manages the Odessa Municipal Airport, got in his own aircraft and flew over the crash scene, which he said looked like a black ink spot on a field.
"There was no sign of an aircraft," he said. "Except there's a pretty deep depression, a hole in the ground, and a lot of debris scattered around."
Much of the plane appeared to have disintegrated on impact.
The Prowler specializes in electronic warfare such as jamming enemy radar and intercepting radio transmissions. It can also be equipped with missiles.
Whidbey Island officials said the plane that crashed was attached to Electronic Attack Squadron VAQ-129.