WASHINGTON — The Department of Justice filed suit Wednesday against Ferguson, Mo., after the city rejected an agreement to overhaul its beleaguered criminal justice system and address allegations of widespread civil rights abuses.

“Their decision leaves us no further choice,’’ Attorney General Loretta E. Lynch said in remarks prepared for a news conference announcing the suit.

Lynch said residents of the city had waited too long for reforms.

“They have waited decades for justice. They should not be forced to wait any longer,’’ she said.

The Ferguson City Council voted 6-0 Tuesday night to reject the deal, which had been negotiated by Department of Justice and city officials. Council members expressed concern over the cost of that deal, but now face the prospect of a lawsuit that could cost millions in legal fees even if they prevail.

Under President Obama, the Justice Department has opened more investigations into patterns of police abuse than it has under any previous administration. The 2014 police shooting of an 18-year-old black man in Ferguson, Michael Brown, set off nationwide protests and attracted the scrutiny of the federal authorities.

The result of that investigation was a scathing Justice Department report, which concluded last year that Ferguson’s criminal justice system was broken at every level. It said police officers used excessive force almost exclusively against African-Americans and did not know the basic standard for making an arrest. Investigators concluded that the city’s Police Department and court operated not as independent bodies but as a moneymaking venture to pad Ferguson’s budget.

After months of negotiating with the Obama administration, city officials tentatively agreed last month on a deal that would have avoided a lawsuit. They agreed that police officers would not make arrests without probable cause, shoot at moving cars, or use stun guns as punishment.

The agreement demanded that the municipal court be independent of the Police Department, and called for the repeal of some laws, like a vague jaywalking ordinance that was used almost exclusively against black residents.

It was an expensive deal. It called for Ferguson to pay for an independent monitor, provide new training, and give raises to police officers in order to attract qualified applicants. Ferguson has been running an operating deficit of about $2.5 million since the unrest of a year and a half ago, but Mayor James Knowles III said he was optimistic that he had the votes in the City Council to approve the agreement.

But at a crowded public hearing Tuesday, things fell apart. Council members and some residents said they could not afford the cost, which could require a tax increase. The city said that giving pay raises to police officers could prompt similar raises for other municipal employees.

Most of the public comments encouraged council members to approve the deal, even if it required tax increases to pay for it.

“A lot of our residents know the situation we’re in and still want the city to sign the consent decree so we can move our city forward, so we can roll up our sleeves and get to work,’’ said Mildred Clines, a Ferguson resident.

With senior Justice Department officials watching from Washington on a video feed, the council voted to reject the deal as written and send it back with changes. Members of the council proposed eliminating the pay raises and, most significantly, striking a provision that would require the city to abide by the deal even if it dissolved the Police Department and turned police duties over to an outside agency.

“This is a way to meet the demands of the DOJ, make progress with reform, and keep lights on in the city,’’ Councilman Wesley Bell said after the vote.

The Justice Department had made it clear that since city negotiators had already agreed on the terms, anything short of a vote for approval would result in a lawsuit. Dan Webb, the city’s lawyer, said this week that if the deal were rejected, there was “no chance the DOJ will not file a lawsuit.’’

Fighting the Justice Department is expensive, which is why it is also rare. In 2012, the Justice Department sued Sheriff Joe Arpaio of Maricopa County, Arizona, over allegations of discrimination against Latino immigrants. Like Ferguson, the county rejected settlement deals and fought the case in court, ringing up about $5 million in legal fees. Three years later, Maricopa County agreed to settle the case.

Ferguson leaders said they had already begun making changes to the city’s police and court procedures. Knowles, for instance, has taken steps to form a civilian oversight panel to review allegations of police abuse. And officials said they would continue making changes, court case or not.

“We don’t feel that we need an agreement to start making reforms and moving forward,’’ Bell said. “If there’s this lawsuit, that’s not going to stop us from moving forward with these reforms.’’