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© Photograph: PAThe MoD is also facing allegations that British forces were responsible for the unlawful killing of more than 250 people who were not in custody.
MoD faces legal challenge to its refusal to hold public inquiry into alleged human rights violations following 2003 invasion

Fresh investigations have been ordered into the deaths of several prisoners who died in suspicious circumstances while under British military custody in Iraq, the high court has been told.

The disclosure comes as the Ministry of Defence faces a legal challenge to its refusal to hold a public inquiry into a series of alleged human rights violations following the 2003 invasion, including hundreds of claims of unlawful detention, torture, and murder.

An inquiry team established by the MoD is now re-investigating the deaths of two men who had been detained by soldiers of the Black Watch in Basra in May 2003, the department's lawyers told the court.

An initial review by the MoD's Iraq Historic Allegations Team (IHat) had concluded that although inquiries had been made following the deaths of Radhi Nama and Jabbar Kareen Ali, "both investigations had not been sufficiently thorough and were thus incomplete" and would need to be re-investigated.

Nama died a few hours after being detained for questioning. Witnesses allege he had been handcuffed before being picked up and hurled into the back of a truck. A former soldier of the Black Watch has said Nama's body was removed from the base while strapped upright in a Land Rover in order that a visiting journalist should not learn about the death. A death certificate was later issued, stating that he had died of natural causes.

Ali, 55, a head teacher suspected of being loyal to Saddam Hussein's regime, died five days later after he and his son Bashar were also detained for "tactical questioning". Bashar alleges they were beaten, hooded, taken to a camp where they were examined by military doctors who did not record their injuries, then hooded and beaten again. He says he heard his father say that he was going to die.

A third case being re-investigated is that of Tariq Sabri al-Fahdawi, who was allegedly kicked to death aboard an RAF Chinook helicopter. Last year an investigation by the Guardian established that the original inquiry by the RAF police had failed to establish the cause of his death, or even his name.

There were claims from senior military sources that MoD officials had interfered in the initial inquiry because they were concerned that any courts martial might result in the disclosure that Sabri - and 63 other men - were being taken to a secret detention centre operated by US and British special forces, a facility that had been concealed not only from the Red Cross, but from the British army's own lawyers.

The MoD says that the new inquiry would be "giving consideration to any involvement with the investigation of MoD officials who were external to it". IHat is also examining six other investigations into deaths in military custody in Iraq before deciding whether these two should be reopened.

Lawyers representing hundreds of Iraqi men who are demanding a public inquiry into allegations they were tortured while being held prisoner by the British say that there is also a need for a transparent examination of suspicious deaths in Iraq.

They say they have identified 13 deaths in British military custody, in addition to that of Baha Mousa, tortured to death by British troops in September 2003.

The true figure could be higher, but is being witheld by the MoD, Michael Fordham QC told the court. "We don't know how many deaths they are aware of and are investigating. We have suggested, a few times now, that they might want to tell the court the truth."

The court has also heard that in addition to the deaths of prisoners, the MoD is facing allegations that British forces were responsible for the unlawful killing of more than 250 people who were not in custody. These include a number of cases described in written evidence to the court as "extra-judicial executions".

Among the cases highlighted in the evidence are that of an eight-year-old girl said to have been shot dead by a soldier from the King's Regiment in August 2002; and an elderly woman who was detained in November 2006 after troops came to her home looking for her son, and whose body was allegedly later found at the side of a road inside a military body bag, with a bullet wound to her abdomen and wounds to her face.

The MoD is resisting a public inquiry, saying it would be "premature and disproportionate" and take much longer than IHat's inquiries. "The MoD takes all allegations of abuse seriously, which is precisely why we set up IHat to ensure that all allegations are, or have been, investigated appropriately," a spokesman said.

Lawyers for the former detainees believe the MoD is resisting a public inquiry because it would uncover evidence that the mistreatment of detainees was "systemic", with those responsible acting in accordance with their training in the UK and orders issued in Iraq.

The court is expected to announce its decision later this year.