Voicing concern over several alleged admissions of guilt, defence lawyers for the 24-year-old Ahmed Omar Abu Ali said on Thursday that his statements were obtained under unacceptable physical and psychological conditions.
Abu Ali confessed to security officials in Riyadh in June 2003, shortly after he was arrested there, and again to FBI and US Secret Service agents, who questioned him over four days in Saudi Arabia in September 2003.
The Virginian suspect's defence team has added that he was tortured by the Saudis at the Americans' behest.
"His torturers did not only inflict on him physical pain in the form of beating and whipping, but used the most sadistic forms of psychological torture as well," write lawyers Ashraf Nubani and Leonard Weinglass in a US district court counter-allegation.
In one case, the Saudis dragged into Abu Ali's interrogation room an elderly man "with clear signs of trauma and abuse. The message was clear: No one was immune from their mistreatment, neither young nor old, guilty nor innocent," the lawyers added.
Abu Ali offered to show a judge scars on his back when he made his initial court appearance in February.
But Washington insists Abu Ali joined al-Qaida in 2002 while studying in Saudi Arabia, where he allegedly discussed numerous potential terrorist acts.
These included plots to kill President George Bush and congressmen as well as a plan to hijack planes in foreign countries and fly them at targets in the US.
However, court records suggest prosecutors are not planning to present evidence of Abu Ali's September 2003 confession at his upcoming trial.
Defence lawyers said that was a tacit admission by the government that the confession was tainted by the FBI agents' acquiescence to torture.
But the prosecution has denied the claim, saying FBI agents questioned Abu Ali without a lawyer, because at the time gathering intelligence about al-Qaida was more important than building a criminal case.