There were no indications that the plane had come under hostile fire and it was not clear if the two aircraft had collided, a US military spokesman said.
"We have not found the second pilot," he said on Tuesday. "The planes were flying too high to be shot down."
The search continued for a second missing crew member, the statement added.
It was unclear how many servicemen had been on board the two jets when contact was lost.
The US military lost contact with two Marine Corps F/A-18 Hornet aircraft in Iraq on Monday at 10.10pm (1810 GMT), a statement said.
The planes were from the USS Carl Vinson, the military added.
A heavy sandstorm and lightning hit central Iraq on Monday night.