In a sign of how bad things have become in Iran, some of those arrested in recent weeks have been relieved to be detained in Evin – a prison in northern Tehran that for decades has been a byword for terror.

It is not that Evin, under the partial control of the fearsome intelligence ministry, has gone soft on the protesters filling its cells since the outbreak of post-election unrest in June. It is just that the options are seen as far worse.

“At least you know you are [being] interrogated by an organisation with relevant obligation in a registered prison, and you are much less likely to be physically tortured,” says one reformist.

Many of those arrested have instead ended up in semi-official institutions, where no reliable arrest records are kept and it is not always clear who is in control.

One centre, Kahrizak, has already been closed on the orders of Ayatollah Ali Khamenei, Iran’s supreme leader, amid allegations of brutal torture.

The Islamic regime was shocked by the extent of the protests over June’s presidential election – the biggest since the 1979 revolution. Hundreds of thousands of demonstrators came on to the streets to denounce as fraudulent the re-election of Mahmoud Ahmadi-Nejad.

The security crackdown that followed – co-ordinated by the police and Revolutionary Guards – saw hundreds detained, including senior reformists. Officially, 20 people died in the clampdown but the opposition claims the figure is far higher. Last week it said 69 people had died, some after being tortured in unregistered detention centres.

The closure of Kahrizak, which is run by the police, came after Mohsen Ruholamini, the son of a senior fundamentalist, was allegedly tortured to death. Esmaeil Ahmadi-Moghaddam, police chief, denied that anyone had died in Kahrizak as a result of torture. He said they had been victims of a “virus”.

The police set up Kahrizak, said to be located below ground, in 2001 to lock up drug smugglers and addicts. Its has since been extended to take in other criminal gang members.

Mehdi Karroubi, an outspoken cleric who was also a presidential candidate, has alleged that at least one woman, Taraneh Moussavi – who is not related to Mir-Hossein Moussavi, the opposition leader – was raped and subsequently died in Kahrizak. He has accused the authorities of trying to cover up the incident.

In a conservative and religious society such as that of Iran, where sex is acceptable only within wedlock or so-called temporary marriages, a charge of rape, in particular against women, would be hugely damaging for the Islamic regime if proved.

Iran’s parliament has said it has investigated the allegations and found them to be baseless. However, that has not quelled fears that similar incidents might be happening in other jails.

Pasargad, a former weapons factory in south-western Tehran, has been highlighted as a detention centre run by the Revolutionary Guards. Some lawyers claim the interior ministry has also established its own jail called “Minus 4”, four storeys under the ground floor of its main building in central Tehran.

Prisoners held at Evin have their names registered but, in these other institutions, this is not believed to be the case. This is one of the main reasons that there are no credible reports about the number of detainees and deaths over the past two months.

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