Up to 200 malnourished Iraqi detainees bearing signs of torture have been found in a secret prison in the basement of a Government building in Baghdad.

The discovery of the prisoners came after American troops surrounded and took control of an Interior Ministry building in the Jadriya neighbourhood of the capital on Sunday night.

When American forces arrived at the facility, officials there told them there were 40 detainees being held. As they moved through the building they discovered at least 200 prisoners, mostly Sunni Arabs and many in very poor health. The Americans had apparently been tipped off to the prison’s existence by relatives of those being detained.

Official announcement of the discovery came just a day after damning United Nations report into the brutal conditions and lack of access to legal counsel in Iraq’s overcrowded jails. The UN Assistance Mission in Iraq expressed concerns about the large number of detainees and suggested that Iraqi police and special forces had abused the human rights of suspects during security sweeps.

But the discovery of an apparently illegal detention centre has raised even more questions over the behaviour of the security forces being primed to take over duties from a withdrawing coalition force.

It also sparked memories of the behaviour of security forces under Saddam Hussein who routinely arrested and tortured prisoners at a variety of secret prisons and detention centres around the city, many of which were not discovered until after his regime fell.

Ibrahim al-Jaafari, the Prime Minister, announced today that there would be an investigation into allegations that Interior Ministry officials had tortured detainees held in the basement prison in connection with the ongoing mostly Sunni insurgency.

"I was informed that there were 173 detainees held at an Interior Ministry prison and they appear to be malnourished." Mr Jaafari told a press conference. "There is also some talk that they were subjected to some kind of torture."

He said that the detainees had been moved to another location and were receiving medical care. American military officials refused to answer any questions about their role in bringing the secret prison to light, referring all inquiries to the Interior Ministry.

Major General Hussein Kamal, the Interior Ministry’s under-secretary for security, confirmed the raid on the building but said all those being held in the facility were "terrorists".

Brigadier General Karl Horst, who commanded the troops that carried out the raid on Sunday night, told reporters that American forces now planned to raid all known detention facilities in the capital.

"We’re going to hit every single one of them, every single one of them," he was quoted as saying by the Los Angeles Times. The raid was among the first known instances in which American forces in Baghdad have stepped in to protect prisoners being held in Iraqi detention.

The discovery will do nothing to calm relations between the country’s warring ethnic groups. Most of the prisoners discovered in the jail were members of the minority Sunni group dominant under Saddam but who make up the backbone of the insurgency fighting the military occupation and the American-backed government.

The Interior Ministry, controlled by Shia Muslims, has been repeatedly accused of using its security forces to detain, torture and kill hundreds of Sunnis simply because of their religious affiliation.

Many of its officials are members of Shia militia forces like the Badr Brigade recently tied to anti-British violence in the south. Police sources said they believed that the Jadriya facility was being run by the Badr brigade as their own personal militia jail.

American officials have been encouraging Sunni Arabs to take part in next month’s parliamentary elections in hopes that a strong turnout by the disaffected minority could help ease sectarian tensions, calm the insurgency and speed the day when foreign troops could go home.

But the discovery of the jail once again throws up more questions about the suitability of Iraqi forces to take on the task of fighting the insurgency while respecting suspects’ human rights.

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