"The Americans assured us that they informed the Baghdad operations centre, but they said 'Our mistake was that we did not inform the police in Kut'," the official said.
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militant groups it suspects of being backed by Iran and the killing of a "network financier" responsible for weapons smuggling.
A woman and a policeman were killed during the pre-dawn operation in the southern town of Kut near the border with Iran.
"This was a kind of breach (of the US-Iraqi security pact) and all the measures we have taken are designed to ensure that this sort of incident does not occur again," defence ministry spokesman Mohammed al-Askari told AFP.
But Iraq on Sunday detained two army commanders after the defence ministry said Baghdad had no knowledge of the operation, and the six suspects arrested by US forces, including a police captain and a tribal leader, were released.
The US military has long accused Iran of supporting sectarian militias in Iraq, a charge Belstaff Bragg Jacket Uk
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Washington or Baghdad had accused the other of violating the Status Of Forces Agreement, which requires US troops to leave all cities by June 30 and completely withdraw from Iraq by the end of 2011.
But on Monday a US military spokesman said that those involved in Sunday's incident were "deeply saddened by the outcome of the operation" and expressed their "deepest condolences for the terrible tragedy."
In June 2008, US forces arrested six men they accused of being part of an Iranian-trained militia in Kut, a mostly Shi'ite town.
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an interior ministry official who was part of a delegation sent to investigate the incident said the Americans apologised for the killings and promised to compensate the family involved.
The US military had earlier insisted that the raid was "fully coordinated and approved by the Iraqi government."
He also demanded that those responsible be "put on trial."
The US military said on Monday it was "deeply saddened" by a deadly raid it launched in Iraq which Baghdad said violated a landmark security pact with Washington.
Iraqi Prime Minister Nuri al-Maliki said the raid was in breach of a security agreement signed with Washington in November that requires that all US military operations be "fully coordinated" with Iraqi authorities.
The pact allows Iraq to try US soldiers under certain circumstances but not for alleged crimes committed during combat missions.
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raid came in the wake of a renewed flare up of violence in Iraq, where at least 150 people were killed in attacks last week, including 65 people who died in a twin suicide bombing on Nike Shox Nz Womens
Friday outside Baghdad's most holy Shi'ite shrine.