UPDATED: 5/9/2011 3:10 p.m.

CHICAGO (CBS) — Federal authorities are investigating the police department in Newark, New Jersey, after the state’s American Civil Liberties Union complained of rampant misconduct and lax internal oversight.

Since 2006, that department has been led by Police Director Garry McCarthy. Last week, McCarthy announced that he’s leaving to take over as Chicago’s police superintendent.

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In September, the ACLU called for federal oversight of the city’s 1,300-officer department. The ACLU found more than 400 complaints over a 2 1/2 year period, with most in the internal affairs division. Of the 261 complaints in that division, only one complaint was found credible, which raises a red-flag for the ACLU.

“There were things that could have been done by then-Director McCarthy, said the ACLU’s Alex Shalom. “But I do want to stress it’s not something he could have solved on his own.”

The problems go back 50 years and the department is in need of major systematic reform, Shalom said.

At a news conference in Newark, McCarthy stood stoically as federal prosecutors spoke of serious allegations of misconduct.

The Justice Department will be look at “whether officers have engaged in excessive force, unlawful traffic stops, searches, arrests or discriminatory policing,” said U.S. Attorney Paul Fishman.

In a statement, mayor-elect Rahm Emanuel sought to firewall is top cop from any blame.

“Before McCarthy’s tenure at the Newark Police Department, there were questions about complaints from the public.” Emanuel said. “As a result, McCarthy instituted aggressive and successful reforms.”

McCarthy said he took action to reverse the generations of problems within the department.

“This is the beginning of the end of this debate,” McCarthy said. “I believe the reforms we put in place will hold up to scrutiny and become the best practices all across the United States.”

Instances of misconduct included officers breaking a man’s jaw and eye socket during an arrest and seven deaths attributed to Newark officers. The deaths included shootings or ignoring urgent health complaints, the ACLU said.

The ACLU petition also said the city had paid $4.8 million over 2 1/2 years to settle 38 cases brought against police by residents or department employees, with at least three dozen lawsuits pending.

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