The investigation comes as Chicago officials announce an officer involved in a second fatal shooting will not be charged.
The US Justice Department will launch a wide-ranging investigation into the Chicago Police Department following the release of a video showing the shooting of a black teenager.
The civil rights probe, which comes after similar investigations in Baltimore and Ferguson, follows intense scrutiny surrounding the police department and Mayor Rahm Emanuel over their handling of the death of 17-year-old Laquan McDonald.
Officer Jason Van Dyke was charged with first-degree murder on 24 November, more than a year after the teenager’s death and hours before police dashboard camera footage showing the fatal shooting was released.
The video showed Mr McDonald moving away from officers when Van Dyke opened fire from close range.
The officer continued shooting after the teenager fell to the ground and stopped moving.
Chicago City Council signed off on a $5m (£3.3m) settlement with Mr McDonald’s family before they had filed a lawsuit and officials fought for months in court to prevent the video, which does not include sound, from being released publicly.
Since its release, Mr Emanuel forced Police Superintendent Garry McCarthy to resign and formed a task force to examine the department.
Chicago police officer Jason Van Dyke is charged in the fatal shooting of 17-year-old Laquan McDonald in 2014
But calls for him to resign have grown during protests around the city.
Early efforts to suppress the release of the footage by the city coincided with Mr Emanuel’s re-election campaign.
US Attorney General Loretta Lynch confirmed the investigation at a news conference on Monday, and said authorities will look at the Chicago police department’s use of force and its accountability systems.
She said: “Our goal in this investigation… is not to focus on individuals but to improve systems.
“We understand that the same systems that fail community members also fail conscientious officers by creating mistrust between law enforcement and the citizens they are sworn to serve and protect.”
City officials last week released documents which showed officers reported different versions of the fatal shooting to that in the video. They also portrayed Mr McDonald as more menacing.
Meanwhile, it was announced on Monday that a second Chicago police officer involved in the fatal shooting of a black man in October 2014 would not face charges.
Cook County State’s Attorney Anita Alvarez also released long sought footage that showed the shooting of Ronald Johnson III.
The 25-year-old was armed with a handgun and running from officers when he was shot in the back by Officer George Hernandez, authorities said.
Ms Alvarez said Johnson had been asked repeatedly by multiple officers to drop his weapon, and that he was running in the direction of other officers in a police vehicle when he was shot.
A 9mm pistol was found next to Johnson, who police have described as a known gang member.
His family has contended that officers planted the gun.
Of 409 shootings involving Chicago police since September 2007, only two have led to allegations against an officer being found credible, the Chicago Tribune reported.