Human rights abuses in Iran are now as bad as at any time in the past 20 years, Amnesty International reports tomorrow in a survey marking six months since June's disputed presidential election.

Amnesty documents "patterns of abuse" by the Basij militia and revolutionary guards involving beatings, rape, death threats, forced confessions, intimidation and official cover-ups. Many detainees have been subjected to show trials and five have been sentenced to death.

"The authorities have resorted to exceptionally high levels of violence and arbitrary measures to stifle protest and dissent," says the 80-page report. "The courts have not been an instrument of justice to hold police, security forces and other state officials to account … or to protect the rights to freedom of expression, assembly, association and religion."

According to official figures, 36 people died in violence after the election, but the opposition puts the figure at more than 70. At least 4,000 people were arrested after the poll on 12 June and some 200 remain in jail. This week, 200 people were arrested during protests around university campuses on national students day.

Protests began when the sitting president, Mahmoud Ahmadinejad, claimed victory over the leading opposition candidate, Mir-Hossein Mousavi, amid claims that the result had been rigged.

Amnesty quotes an unnamed former detainee who was held with 75 others for more than eight weeks in a container at the notorious Kahrizak detention centre in Tehran. He was told his son would be raped if he did not "confess" and was beaten unconscious with a baton .

Last month, Ramin Pourandarjani, a young doctor who had treated inmates at Kahrizak and had reportedly been forced to certify the death of at least one torture victim as resulting from meningitis, died in suspicious circumstances.

Ebrahim Mehtari, a 26-year-old student, described being held in a tiny cell, interrogated while blindfolded and accused of "working with Facebook networks" and tortured into making a confession. He said: "They frequently beat me on the face; I was burned with cigarettes under my eyes, on the neck, head. I was beaten all over … They threatened to execute me and they humiliated me."

An independent medical examination substantiated his claims. But all the relevant documents disappeared, the authorities refused to investigate and his family were warned not to talk about the case.

Amnesty says Iran refused to co-operate with its investigation and has denied the organisation entry into the country since the 1979 Islamic revolution.

Many of the cases have been documented previously, but the cumulative effect of the data underlines what Amnesty calls "a clear pattern of systematic gross human rights violations by Iranian security forces condoned or even encouraged by powerful political and religious figures in Iran."

The report says government officials "have done their utmost to ensure that accounts of rape are discredited and not circulated further".

Amnesty has harsh words for the show trials of leading opposition figures. "The trials, broadcast to the nation, featured coerced 'confessions', 'apologies' and incrimination of others. Rather than bringing people to justice, the purpose was to validate the authorities' account of the post-election unrest and to make clear the severe consequences of opposing the authorities."

• The caption to the picture with this article was amended on Wednesday 10 December 2009. Mashhad is in north-east Iran, not north-west as it originally said. This has been corrected.