The motion comes more than a week after a military prosecutor overseeing Sinclair's case abruptly left the case.
Sinclair, 51, has pleaded not guilty to eight criminal charges including forcible sodomy, indecent acts, violating orders and conduct unbecoming an officer. He faces a maximum sentence of life in prison at a court-martial that was scheduled to begin March 3.
The married father of three has admitted to having an extramarital affair with a female captain under his command, but maintains the relationship was consensual.
Military officials said last week that lead prosecutor Lt. Col. William Helixon had left Sinclair's case "for personal reasons."
But in the motion filed by Sinclair's defense Friday, Helixon is quoted telling a superior that he has doubts about the credibility of Sinclair's accuser.
It says on February 8, 2014, Helixon shared with lead defense attorney Richard Scheff that "he believed (the accuser) had lied, and that charges that relied solely on (the accuser) should be dismissed."
The introduction to the motion describes how Helixon felt ethically bound to remove himself from the case after concluding there was reasonable doubt as to Sinclair's guilt on the sexual misconduct charges. It goes on to say he was ignored or rejected by the Staff Judge Advocate and Convening Authority, and concludes that "the decision-makers in this case fear the adverse personal and political consequences of taking the ethically, morally and just action of dismissing the charges that rely on the Government's discredited primary accuser." It ends by saying the case should be dismissed as a result of "unlawful command influence."
The motion also claims that Helixon has disclosed that General Ray Odierno, the Army's top commander, is "aware that the charges relying on the captain's testimony are likely to fail."
During a February 9 phone conversation between Helixon and Scheff, the motion says Helixon "acknowledged Sinclair was not guilty of sexual misconduct charges, nor did he deserve to be dismissed from the Army, go to jail or register as a sex offender." It says Helixon believed that "politics and outside pressures were driving forces pushing the case forward," telling Scheff that former 18th Airborne Corps SJA, Brigadier General Paul Wilson, would be "in charge" of the prosecution.
Wilson is currently a Washington, D.C.-based Assistant JAG for Military and Operational Law. The motion goes on to say that Wilson told Helixon he "knew the accuser was a liar, that she had lied since the beginning, and that she'd repeatedly lied directly to Helixon."
Wilson, Helixon, current 18th Airborne Commander Lt. General Joseph Anderson, public affairs staff and many other are requested to testify in a hearing, according to the motion.
Sinclair's defense has portrayed the woman as a jealous ex-lover and challenged her testimony - asking that she be charged with perjury after questions were raised about evidence she said she found on a cell phone.
Sinclair has reportedly offered to plead guilty to some of the less serious charges against him. An admission of adultery alone would almost certainly end his 28-year Army career - as adultery is a crime under military law. Fort Bragg officials rejected the plea offer in December.
As deputy commander of the 82nd Airborne, Sinclair oversaw 22,000 troops until he was abruptly sent home from Afghanistan last year and criminally charged.
The case has made national news as the military has faced accusations that it not done enough about sexual assault cases in its ranks.
Fort Bragg officials have not said if the latest developments in the case could mean a delay. The case is still currently set to go to court in March.