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WASHINGTON — Just weeks before Blackwater guards fatally shot 17 civilians at Baghdad’s Nisour Square in 2007, the State Department began investigating the security contractor’s operations in Iraq.

But the inquiry was abandoned after Blackwater’s top manager said: “he could kill” the government’s chief investigator and “no one could or would do anything about it as we were in Iraq,” according to department reports.

U.S. Embassy officials in Baghdad sided with Blackwater rather than the State Department investigators as a dispute over the probe escalated in August 2007, the previously undisclosed documents show. The officials said they had disrupted the embassy’s relationship with Blackwater and ordered them to leave the country, according to the reports.

After returning to Washington, the chief investigator wrote a scathing report to State Department officials documenting misconduct and warning that lax oversight of the company, which had a contract worth more than $1 billion to protect U.S. diplomats, had created “an environment full of liability and negligence.”

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“Blackwater contractors saw themselves as above the law,” Jean Richter wrote in an Aug. 31, 2007, memo to State Department officials, adding that the “hands off” management resulted in a situation in which “the contractors, instead of Department officials, are in command and in control.”

His memo and other newly disclosed State Department documents make clear that the department was alerted to serious problems involving Blackwater and its government overseers before the Nisour Square shooting.

Today, as conflict rages again in Iraq, four Blackwater guards involved in the Nisour Square shooting are on trial in Washington on charges stemming from the episode, the government’s second attempt to prosecute the case in a U.S. court after previous charges were dismissed in 2009.

The shooting was a watershed moment in the U.S. occupation of Iraq, and was a factor in Iraq’s refusal the next year to agree to a treaty allowing U.S. troops to stay beyond 2011.

The State Department declined to comment on the aborted investigation. A spokesman for Erik Prince, the founder and former chief executive of Blackwater, who sold the company in 2010, said Prince had never been told about the matter.

After Prince sold the company, the new owners named it Academi. In early June, it merged with Triple Canopy and is now called Constellis Holdings.

Experts who were previously unaware of this episode said it fit into a larger pattern of behavior.

Even before Nisour Square, Blackwater’s security guards had acquired a reputation among Iraqis and U.S. military personnel for swagger and recklessness, but their complaints about practices ranging from running cars off the road to shooting wildly in the streets and even killing civilians typically did not result in serious action by the United States or the Iraqi government.

But scrutiny of the company intensified after a Blackwater convoy fired on Nisour Square on Sept. 16, 2007. A 9-year-old boy was among the civilians killed.

Blackwater guards later claimed that they had been fired upon first, but U.S. military officials who inspected the scene determined there was no evidence of any insurgent activity there that day.

Federal prosecutors later said Blackwater personnel had shot indiscriminately.

Founded in 1997 by Prince, a former member of the Navy SEALs and an heir to an auto-parts fortune, Blackwater began as a small company providing shooting ranges and training facilities in rural North Carolina for the military and for police departments. After the U.S.-led invasion of Afghanistan and later Iraq, it ramped up to become a global security contractor with billions of dollars in contracts for the State Department and the Central Intelligence Agency.

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