The men had left their base near the southern Iraqi city of Basra to carry out reconnaissance and supply a second patrol with “more tools and fire power”, said a source with knowledge of their activities.

They had been in Basra for seven weeks on an operation prompted by intelligence that a new type of roadside bomb which has been used against British troops was among weapons being smuggled over the Iranian border.

The bombs, designed to pierce the armour beneath coalition vehicles, are similar to ones supplied by Iran to Hezbollah, the Islamic militant group.

“Since the increase in attacks against UK forces two months ago, a 24-strong SAS team has been working out of Basra to provide a safety net to stop the bombers getting into the city from Iran,” said one source. “The aim is to identify routes used by insurgents and either capture or kill them.”

The forces have tried to seal the notoriously porous border using high-technology sensors that monitor movement by night. They report to a major based in Baghdad in an unmarked building known as the “station house”.

Special forces commanders believe that a tip-off from a local worker at their base may have led to the men’s capture last Monday after a car chase by police, who later handed them to the Mahdi army of Moqtada al-Sadr, the maverick Shi’ite cleric. They were freed from a nearby house.

The disclosure that the SAS has targeted the Iranian border coincides with claims by a former Iraqi defence minister that parts of Iraq have fallen under Tehran’s control.

Hazim Shalan, who left office last May amid a scandal over huge sums of missing money, claimed that 460 Iranian agents had been apprehended in the past two years. He accused Iranian officials of bringing weapons and drugs into Iraq and of paying voters to back their chosen candidates.

An inquiry into the capture of the SAS team and clashes that followed between British forces and an Iraqi mob was being carried out by the Royal Military Police Special Investigation Branch.

The Ministry of Defence (MoD) said this would focus on how the soldiers had been compromised but it was also expected to address claims that they had shot an Iraqi police officer.

The officer, Quteeb Rasheed Abdul Hameed, alleged that he had been wounded in the leg when the soldiers opened fire as police approached their unmarked car to question them.

A judge said yesterday that he had issued warrants for the arrest of the SAS men over the shooting and the alleged killing of a second man shot in the car chase. Judge Ragheb Mohamad Hassan al-Muthafar told The Sunday Times in an exclusive interview that the soldiers were “suspects who attempted to commit a wilful act of murder”.

He added: “Whatever their mission they have no right to fire intentionally on anyone, let alone a security man whose job is to protect this country.”

According to the judge, nine people were killed and 14 injured, including two boys aged 13 and 14, when the mob attacked British forces surrounding the police station where the men were detained.

The MoD declined to comment on the toll but said the warrants had no legal basis. “All British troops in Iraq come under the jurisdiction of Britain,” a spokesman said.

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