Mahmoud Shammam, a Libyan official said that most of the prisoners were not under the control of the interim government, but were under semi-autonomous groups of fighters.
"We have a lot of problems in the prisons," said Shammam, Information Minister.
Human rights has also reported on the mistreatment of detainees in jail run by former rebels.
Reports reveal that the national assembly will be set up in about eight months and prepare for further elections and a new constitution.
"The clock is ticking, and we have to move faster than we are doing right now," said Shammam.
"Perhaps we can shorten this period of time, so Libyans can quickly select their national congress," said Abdul-Jalil, head of the National Transitional Council.
Angry relatives of slain Gaddafi loyalists protested outside a prison in Tajoura and demanded that the detainees be freed for Eid al-Adha, Muslim holiday. A list of names posted outside the prison said that at least 1,000 detainees were being held at the prison.
53-year-old Salah Shambob said that he met two of his cousins in the jail. He further said that his cousin was kept in a small bathroom prison for a month with his hand cuffed to a wall and his head was doused in a toilet during interrogation.
The relatives also said that the detainees were beaten especially after the guards got drunk and the prison cells were crowded.
One such prisoner who was released after 50 days said that his prison mate received electric shocks.