A former imam of the Khoja Nuriddin mosque in Tashkent, Fahrutdinov is charged with terrorism and extremist and anticonstitutional activities, among other crimes.
Fahrutdinov, who had been missing since 1998, was detained in southern Kazakhstan in November, along with eight other Uzbeks. All were subsequently extradited to Uzbekistan.
Four of them had already registered with the United Nation's refugee agency, the UNHCR, in Almaty, seeking political asylum.
Fahrutdinov's wife, Muhayo Ismoilova, alleged earlier this month that the couple's six-year-old daughter had been raped by an Uzbek security service officer, forcing Fahrutdinov to confess to committing the crimes.
Uzbek police denied the allegations and subsequently arrested and charged 16-year-old Nigmatulla Qalandarov with committing the rape. He was tried and sentenced to nine years in prison.