Mayor Stephanie Rawlings-Blake said even though complaints of excessive force and lawsuits alleging misconduct are down over the last few years, "we all know that Baltimore continues to have a fractured relationship between the police and the community."
The mayor's request came a day after new Attorney General Loretta Lynch visited the city and pledged to improve the police department, telling faith and community leaders "we're here to hold your hands and provide support."
Baltimore saw days of unrest after Freddie Gray, a black man, was taken into custody and suffered critical injuries. He died a week later. Protesters threw bottles and bricks at police during a riot on April 27, injuring nearly 100 officers. More than 200 people were arrested as cars and businesses burned.
A Baltimore Police Department spokesman had no immediate response to the mayor's request. An email and text message was not immediately returned.
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The Justice Department is already investigating whether Gray's civil rights were violated, and six officers face charges in the arrest and death, ranging from assault to second-degree murder.
The new investigation the mayor called for is similar to one was done in Ferguson, Missouri, following the shooting of an unarmed, black 18-year-old man by a white police officer.
Such wide-ranging investigations look for patterns of discrimination within a police department. They can examine how officers use force and search and arrest suspects.
Baltimore City Council President Jack Young has been calling for such an investigation since October, his spokesman Lester Davis said.