The investigation aims to identify any patterns of unlawful policing, officials said.
Chauvin faces up to 40 years in prison after what was the first conviction of a white police officer over the death of a black suspect in the state of Minnesota’s history.
Three other officers facing charges in Floyd’s death, Tou Thao, J Alexander Kueng and Thomas Lane, are expected to go on trial in August.
The probe will look into the use of force by police officers, including during the widespread Black Lives Matter protests after the murder, and whether Minneapolis police engage in discriminatory practices.
“Yesterday’s verdict in the state criminal trial does not address potentially systemic policing issues in Minneapolis,” US attorney general Merrick Garland said.
“The justice department has opened a civil investigation to determine whether the Minneapolis police department has engaged in a pattern and practice of unconstitutional or unlawful policing.
“The challenges we face are deeply woven into our history. They did not arise today, or last year; building trust between community and law enforcement will take time and effort by all of us,” Garland said at Justice Department headquarters.
“But we undertake this task with determination and urgency, knowing that change cannot wait.”
The new investigation is known as a “pattern or practice” — examining whether there is a pattern or practice of unconstitutional or unlawful policing — and will be a more sweeping review of the entire police department. It may result in major changes to policing in the Minnesota city.
It will also look into the department’s handling of misconduct allegations and its treatment of people with behavioural health issues and will assess the department’s current systems of accountability, Garland said.
The Minneapolis police said in a statement that chief Medaria Arradondo “welcomes this investigation” and will fully co-operate with federal prosecutors.
Law officials showed bodycam footage at a news conference of an officer shooting the girl in Columbus after she appears to charge with a knife at two people outside a house in a residential street.
On-lookers in the video can be heard shouting “she’s just a kid,” before moving away to give police room to check the teenager’s wounds.
President Joe Biden hailed the guilty verdicts against Chauvin as a “giant step forward” for America in the fight against systemic racism.
Mr Floyd’s grieving family called the landmark verdict a “turning point in history” and received a call from Mr Biden, who promised to tackle racism across the US.
Prime Minister Boris Johnson and former US President Barack Obama were among the world leaders who welcomed the jury’s verdict.
Mr Floyd was being arrested on May 25 last year on suspicion of using a counterfeit $20 note at a grocery store when he was pinned down by police with Chauvin’s knee on his neck for nine minutes and 29 seconds.
Harrowing video footage captured the killing, as Mr Floyd called out “I can’t breathe” 27 times and Chauvin refused to relent to allow medical assistance.
Chauvin, sacked as a police officer following the death of Mr Floyd, was handcuffed and remanded in custody immediately after being found guilty of murder.
He faces up to 40 years in prison at sentencing in eight weeks’ time.
State prosecutors are expected to argue for significantly more than the 12-and-a-half year benchmark for second-degree murder in Minnesota guidelines.
Chauvin, currently being held at maximum-security Oak Park Heights prison 25 miles outside Minneapolis.
He is also expected to appeal his convictions, arguing his trial was unfair due to the timing and location, as well as media coverage.
He is also likely to argue jurors were tainted by a $27 million (£19 million) payout to Mr Floyd’s family, controversially announced just before the trial began.