FBI arrested Dr Fai on July 19 on the charges of his alleged links with Pakistan's spy agency while try to influence US lawmakers.
The court ruled that Dr Fai would remain under house arrest during the trial. Meanwhile, passport of the accused and her wife would remain in the court custody.
During the hearing, Defense lawyer Nina Ginsberg denied the allegations against Dr Fai.
Fai, who did not say anything during the hearing, faces up to five years in prison if convicted. No date has been set for his trial.