The 300 handwritten pages were seized when Qanimat Zahid, editor in chief of the opposition "Azadliq" newspaper, was transferred from the pretrial detention center to the prison. Zahid's lawyers say prison officials have refused to give the papers back.
A spokesman of the State Penitentiary Service said, "We don't interfere with the prisoners' intellectual activity, but each prison has its own rules and they have to be followed." He said this issue would be resolved in court.
In an interview with RFE/RL's Azerbaijani Service, "Azadliq" deputy editor Azer Ahmedov quoted prison officials as saying the manuscript had been destroyed.
The trial is to resume on August 14.
Zahid is serving a four-year sentence for "aggravated hooliganism" and assault and battery in connection with a 2007 incident in which he was accosted by a stranger.
Zahid's brother, Mirza Sakit, an "Azadliq" correspondent, is currently serving a three-year jail term on similar charges.