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UK raid angers Basra politicians
Basra City Council has withdrawn co-operation from UK forces in southern Iraq after the police's serious crimes unit was disbanded by troops.
More than 1,000 troops helped to break-up the unit, which has been blamed for robberies and death squads.
Major Charlie Burbridge said local politics was "complicated" and targeting the unit had been justified.
Mohammed al Abadi, head of the city's council, said the raid was provocative and illegal.
During the operation, troops stormed the unit's headquarters and took charge of 127 prisoners whom they feared might be killed.
They demolished the Jamiat police station, which was the Serious Crimes Unit's base in Basra.
Soldiers from 19 Light Brigade supported by Iraqi forces surrounded the police station before the Royal Engineers used a combat tractor to breach the walls.
Then, warrior vehicles from Staffordshire Regiments entered the compound and troops stormed the buildings.
Major Burbridge, speaking on behalf of the British Army in Basra, said: "The local provincial council, or a few members of the local provincial council, conducted a press conference a couple of hours after the operation was completed and they criticised the way in which, or the means by which, we conducted the operation.
"Now let's say we put this in context. Of course the local political scene is a complicated one and the governor [Mohammed al-Waili] wasn't there at the press conference."
The major added: "He [Mohammed al-Waili] even had a conversation with our general and said that we had done the right thing.
"Furthermore, we have continued to have overwhelming support up in Baghdad from the Ministry of Defence, so we're pretty confident we've done the right thing here."
But Mr al Abadi said local officials had not been informed of the operation and that it violated earlier agreements to move the prisoners without military action.
British forces have said they were forced to move sooner than expected after receiving intelligence reports suggesting that police were planning to execute their prisoners.
A Ministry of Defence spokesman said hundreds of seized files and computers were taken as evidence.
The raid came three days after seven Iraqi officers were arrested on suspicion of corruption and leading a death squad at the unit.
Maj Burbridge added: "For some time we've been talking about culling the police force; well, this is exactly what we've done.
"We've removed a very significant and nasty part of the police force which has been scaring people in Basra and ultimately it's going to make Basra a better place."
Troops carried out medical assessments of detainees before transferring them to another police station, and said there was evidence of torture.
Some had crushed hands and feet, and electricity burns and gunshot wounds to the legs, they said.
A military operation at Jamiat in September last year rescued two British soldiers - arrested for allegedly shooting dead a policeman and wounding another - sparking unrest in which Army vehicles were attacked.
There have been long-held fears of the Iraqi police being infiltrated by corrupt officers.
And British forces have said some Iraqi commanders were using the unit as a cover for death squads and criminal activities.
Basra, Iraq's second biggest city, remains dangerous, with Shia factions battling each other for control.
The UK has 7,200 troops in the south of Iraq, mostly in the Basra area.