While Lamar Johnson has spent 24 years in a Missouri prison, evidence of his innocence has steadily mounted. Two other men who confessed to the murder attributed to Mr. Johnson said he did not do it. And the only eyewitness against him — without whom prosecutors said they had no case — later recanted.

This year, after his fruitless declarations of innocence from behind bars, prosecutors from the same office that sent him away for life in 1995 decided that he was innocent and asked a judge to grant him a new trial. The response was swift and not in Mr. Johnson’s favor: The Missouri attorney general weighed in, helping convince the judge to deny the request.

The pushback faced by prosecutors in Mr. Johnson’s case is not unique. Across the country, similar clashes are playing out as prosecutors who were elected in recent years promising a different approach to criminal justice have seen some of their efforts frustrated. Opponents with a more traditional view of law and order are taking concrete steps to try to block them in court and strip them of discretion or money to run their offices.

From the start, these prosecutors met fierce criticism from law enforcement and other elected officials when they promised to crack down on police misconduct, prosecute fewer nonviolent crimes and reverse potentially wrongful convictions.

This month, Chesa Boudin, a former public defender, eked out a narrow victory in San Francisco after pledging wide-ranging reforms. The city’s police union had spent more than $600,000 on ads opposing Mr. Boudin, declaring him the “#1 choice of criminals and gang members.”

For decades, district attorneys enjoyed almost unlimited discretion in how they could pursue cases. Most of them used that authority to send more and more defendants to prison, helping to drive the nation’s incarceration boom.

What is now at stake is the latitude of prosecutors to make decisions meant to slow, instead of accelerate, the pipeline to prison. Experts say more conflicts are sure to emerge between prosecutors elected in mid-to-large-size cities, where a new approach is popular, and state officials who answer to a wider electorate that does not favor such sweeping reforms.

“When D.A.s were ramping up, no one had a problem,” said Miriam Krinsky, a former federal prosecutor who is executive director of Fair and Just Prosecution, an umbrella group of district attorneys seeking change. “Now we’re in a different moment, where some are trying to de-incarcerate, and some people invested in the status quo are trying to clip their wings.”

The pushback could have major implications, both for the role of prosecutors and individual cases. If the judge’s ruling in Mr. Johnson’s case in St. Louis is upheld on appeal, for example, it could make it almost impossible for prosecutors in Missouri to reopen similar cases in the future, no matter how persuasive the new evidence.

Critics of the new cohort of prosecutors, such as William P. Barr, the attorney general, say their efforts are demoralizing to law enforcement and dangerous to public safety. In a speech in August, Mr. Barr criticized “district attorneys that style themselves as social justice reformers, who spend their time undercutting the police, letting criminals off the hook and refusing to enforce the law.”

Removing prosecutors’ authority

What is now being tested is how far prosecutors can go in their new approach to criminal justice, both legally and politically.

In Pennsylvania, legislators passed a bill this summer targeting the handling of gun cases by the Philadelphia district attorney, Larry Krasner. The law gave the state attorney general, Josh Shapiro, the power to prosecute some charges on his own, regardless of input from the local prosecutor’s office.

Activists called the law — which only applies in Philadelphia — a bald attempt to curb discretion that lawfully belongs to Mr. Krasner, a Democrat elected in 2017 by three-quarters of voters. After an outcry, Mr. Shapiro, also a Democrat, said he would support repealing the measure.

Mr. Krasner has also faced pushback from the Trump administration for supporting a site where people could inject opioid drugs while being overseen by medical professionals. The district attorney says the plan would prevent deaths and connect opioid users with treatment options. The Justice Department lost a bid to block the plan last month, but it warned that officials elsewhere would face “immediate action” if they opened similar sites while the case is being appealed.

In Maryland, Gov. Larry Hogan, has faced off with the state’s attorney in Baltimore, Marilyn Mosby, who took office in 2015. Mr. Hogan, a Republican, said she was dropping too many cases and ordered the state attorney general to start prosecuting violent crimes in the city.

In Nashville, Glenn Funk, a Democrat elected district attorney in 2014, agreed to reduce the death sentence of Abu-Ali Abdur’Rahman, who was convicted in 1987 of a fatal stabbing, to life in prison. Mr. Funk cited “overt” racial bias during jury selection.

But the Tennessee attorney general, Herbert Slatery, a Republican, is arguing that taking Mr. Abdur’Rahman off death row would be “essentially granting clemency through a court and a district attorney that both lack the authority to do so.” The case is now before an appeals court, with Mr. Abdur’Rahman’s execution set for April.

In other cities, prosecutors have beaten back efforts to curb their discretion. The Massachusetts Supreme Judicial Court sided with Rachael Rollins, a Democrat elected district attorney in Boston last year, in a dispute with a local judge who did not want to let her dismiss disorderly conduct charges against a protester. The court noted that “sole authority to determine which cases to prosecute” had been her office’s prerogative since the early 19th century.

And Mark Dupree, a Democrat elected district attorney in Kansas City, Kan., in 2016, recently won funding for an office to review potentially wrongful convictions — similar to the office in St. Louis that re-examined Mr. Johnson’s murder case.

A ‘vengeful response’

An early test of prosecutorial power played out in Orlando, Fla., after the 2016 election of Aramis Ayala as state attorney. Ms. Ayala, a Democrat, announced that she would not seek any death sentences in her two-county circuit.

Rick Scott, a Republican who was then the governor, swiftly began transferring about 30 potential capital cases to a neighboring prosecutor.

Ms. Ayala sued, arguing that the death penalty had failed as a deterrent. But the State Supreme Court upheld Mr. Scott’s actions by a 5-to-2 vote. The opinion, written by a Scott appointee, stated that by effectively abolishing the death penalty in her circuit, Ms. Ayala had “exercised no discretion at all.”

State legislators also slashed $1.3 million from her budget. In an interview, Ms. Ayala said that amount was far more than her office would have needed to handle those cases, and that losing it took money away from other initiatives.

“There is this very strong, somewhat vengeful response to a redefining of justice,” Ms. Ayala said. She characterized the funding cut as retribution from lawmakers who wanted to send the message that “deciding to think outside the box is going to be penalized.”

She said the court’s ruling factored into her recent decision not to seek re-election.

‘Clear and convincing evidence’

The clash in St. Louis over Mr. Johnson is now before a state appeals court. He was convicted in the 1994 killing of Marcus Boyd by two gunmen who wore ski masks covering their faces. There was one eyewitness, Greg Elking, who later recanted.

When the conviction integrity unit created by the new circuit attorney in St. Louis, Kimberly Gardner, began looking into Mr. Johnson’s case, it discovered evidence that the police arranged to pay $4,200 to cover Mr. Elking’s utilities, moving bills and other expenses.

A report issued by the prosecutor’s office in July surfaced other serious concerns about the case, concluding that Mr. Johnson had a strong alibi. The other convicted gunman, as well as another man, had also each confessed to being the real killers and swore that Mr. Johnson was innocent.

The prosecutor who handled the case in 1995, Dwight Warren, who is now retired, called the report “utter nonsense and ridiculous.” But he said in an interview that he most likely would not have charged Mr. Johnson without Mr. Elking as a witness.

He said the payments made for Mr. Elking were not bribes to get him to testify against Mr. Johnson — they were for relocating a witness who had feared that he was under threat. “I have been honorable,” Mr. Warren said. “I am not one of these people who is trying to railroad somebody.”

Three months ago, a judge rejected Ms. Gardner’s request to grant Mr. Johnson a new trial, ruling that Missouri law requires such petitions to be filed within 15 days of conviction. The judge also said the circuit attorney’s office had a potential conflict of interest in the case because it was accusing a prior employee of prosecutorial misconduct.

Lindsay Runnels, a lawyer working in partnership with the Midwest Innocence Project, which investigated Mr. Johnson’s case for years before turning its findings over to St. Louis prosecutors, said courts in Missouri have made it clear that judges can bypass the 15-day rule to correct “manifest injustice” or cases tainted by significant perjury.

She also said that every case in which district attorneys seek to correct prosecutorial misconduct would — by definition — involve questioning the actions of someone from their office. Yet prosecutors who fail to re-examine cases where serious evidence of innocence has emerged risk running afoul of legal ethics rules.

“There is clear and convincing evidence that he didn’t do it,” said Ms. Runnels, who is handling Mr. Johnson’s appeal, “and there is no statute of limitations on innocence.”

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