The Airforce Times reports a top general told lawmakers the two pilots are protected under the Federal Whistleblower Act.
One of the pilots Captain Josh Wilson is facing a disciplinary hearing for refusing to fly the plane.
The other, Major Jeremy Gordon, was placed on a do-not fly list for medical reasons.
The Virginia fighter pilots told CBS's "60 Minutes" they refused to fly the jets, because the planes are making them sick.
They say they’ve experienced hypoxia or oxygen deprivation.
A report filed by the Department of Defense Inspector General just made public, shows more than half of all whistleblower cases in the military are mishandled.
The department objects to actions taken in most cases by the military's reprisal investigation unit.
The report goes on to say not all cases found objectionable were to the detriment of the whistleblower.