The report says a legal order banning torture had been ignored. It says arrests were made without sufficient evidence. In some cases suspects were held in undeclared detention centers.
It highlights the case of a 13-year-old boy who was held for a week in a detention center for stealing a hen. It also highlights the case of a 73-old-year woman who was held in prison for four months because she had no money. The report says the judiciary discovered a man who had been in prison more than 15 years without ever having a verdict issued against him.
But now judiciary officials say real reforms have been achieved and the problems have been removed. Hojatoleslam Abbasali Alizadeh says Iran's prisons are now among the best in the world.
Some observers remain skeptical.
Hassan Zarezadeh is in charge of the Student Committee In Defense Of Political Prisoners In Iran. He says the hard-line judiciary is trying to portray itself in a better light.
"[The report] shows that the regime wants to demonstrate that there have been real reforms in the judiciary and that they are committed to human rights," Zarezadeh told RFE/RL. "But their comments about torture being eradicated can be challenged because why are [prisoners] still being held in solitary confinement for long periods while facing complicated interrogations? Isn't it torture? Last week Behrouz Javid Tehrani, a member of the Democratic Party of Iran who has been held in solitary confinement for the last three months, managed to tell his relatives during a visit that he was severely beaten in prison."
Zarezadeh, who has been arrested several times in recent years, says he has witnessed the ill treatment of prisoners. "It includes long solitary confinements, hanging suspects [from the ceiling], handcuffing behind the back, beating, hitting the head of suspects to the wall and also psychological torture," he said.
Mohammad Ali Dadkhah is the spokesperson of the Center of Human Rights Defendants, founded by Nobel Peace Prize Laureate Shirin Ebadi. He says he too believes prisoners' rights are still being violated.
"The bitter reality is that these incidents have existed in our prisons. For example, when I was detained in Evin prison, I was once stripped naked in the snow," Dadkhah said. "I think illegal actions are still widespread in the prisons. As I speak to you, [jailed investigative journalist] Akbar Ganji has not the right to meet his lawyer."
Iranian authorities have in the past denied the mistreatment of prisoners and the use of torture. But human rights organizations have repeatedly said that torture is prevalent in prisons.
Several political prisoners including student activists and journalists have said that they were forced into false confessions under duress. Many have say they have been denied access to relatives and lawyers.
Last year the head of Iran's judiciary, Ayatollah Mahmud Hashemi-Shahrudi, ordered a ban on torture for obtaining confessions. The move was considered a tacit acknowledgement that torture was used in the Islamic Republic.
The Iranian government has welcomed the judiciary report.
But Zarezadeh expresses doubt the report will have real consequences.
"If the Islamic Republic has been forced into a retreat under protests from inside the country and international pressure, it does not mean that torture does not exist, that solitary confinement [will] be eradicated, that all the political prisoners [will] be freed and that other prisoners [will] be treated humanely," Zarezadeh said.
The use of torture in some of Iran's prisons was highlighted by the case of Zahra Kazemi, an Iranian-Canadian photojournalist who died in 2003 after being detained in front of Tehran's notorious Evin prison. According to a government investigation she was struck on the head during interrogations.
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