San Francisco District Attorney Chesa Boudin’s decision to withdraw criminal charges last week against a man who was shot by police after allegedly attacking officers with a bottle has inflamed a simmering conflict between the city’s new progressive prosecutor and the law enforcement groups that opposed his election.

The city’s police union accused Boudin — a former public defender — of giving a “green light” to criminals to attack police, and on Monday called on the federal government to prosecute Jamaica Hampton, the 24-year-old man accused in the Dec. 7 attack in the Mission District. Hampton remains hospitalized and recently had his leg amputated after being shot three times, officials said.

The district attorney’s office, though, said there is nothing conclusive about its decision Friday to pull back the charges “without prejudice,”meaning they can be refiled anytime in the next three years. The office said it suspended the charges as part of a new policy aimed at avoiding conflicts between officer-involved shooting investigations and parallel criminal probes.

The case has quickly become the latest public struggle between San Francisco’s new district attorney, who was sworn in Jan. 8 after campaigning on a platform to be tougher on cops in cases of excessive force, and the Police Department’s rank-and-file. The police union opposed Boudin’s candidacy over fears he would not support law enforcement and be too lenient on criminals.

“The Hampton case is unique because there are multiple victims who are seeking, and who deserve, justice,” district attorney spokeswoman Paula Lehman-Ewing wrote in a statement Monday. “No conclusions about the prosecutorial viability of Hampton’s case should be drawn here.”

Tony Montoya, president of the San Francisco Police Officers Association, called Boudin’s decision “a morale buster” and said the new district attorney is “treating the police like criminals rather than the person who caused the shooting to happen.”

“Mr. Boudin has made it clear to criminals everywhere that you can violently attack a police officer and he’ll look the other way,” said Montoya, who’s in a tight race for re-election and has been criticized by the union’s former brash leaders as being “too soft.”

He spoke Monday morning while flanked by members of the San Jose and Los Angeles police unions. Montoya also announced a new website called BoudinBlunders.com, where he said people can submit tips whenever the new district attorney is “protecting criminals and suspects over crime victims.”

Video of the encounter showed Hampton dodging two San Francisco police officers he had allegedly attacked with a bottle near the intersection of 23rd and Mission streets.

During the foot chase, Hampton appeared to run toward Officer Sterling Hayes, while still carrying the bottle, moments before the officer opened fire. Hampton attempted to get up when Officer Christopher Flores fired one shot.

Police said Hampton matched the description of an intruder who had broken into a woman’s home that morning.

Flores’ attorney, Nicole Pifari, sent a sharply worded letter to Boudin on Monday urging him to reconsider. “Despite the vast spectrum of political beliefs represented in San Francisco, we should hopefully be able to agree that no one is safe in a city where uniformed police officers are attacked and beaten without consequence,” she wrote.

Boudin’s office said his decision to pull back the charges is not unique to Hampton’s case, but rather, is part of a “deconfliction policy” to sort out cases where there is potential for competing criminal liability.

Hampton was originally booked on charges of assault with a deadly weapon, assault upon a police officer and threats to an officer. The case was charged by interim District Attorney Suzy Loftus but never proceeded to arraignment while Hampton remained hospitalized.

“It would be unfair to ask the officers to testify as witnesses in a criminal prosecution while they are still under investigation for their use of force in the same incident,” Lehman-Ewing wrote. “A better approach is to conclude all investigations and proceed with clarity for all involved, witnesses, victims and suspects.”

Robert Weisberg, director of the Stanford Criminal Justice Center, noted the parallel investigations in the case, but said, “It’s not clear that one charge on one side implicates the other.”

“You have two potential criminal cases here and in theory they both could be innocent and they both could be guilty,” Weisberg said. “Assuming it was a tactical decision by Boudin, for whatever reason, you have to balance that against the difficulties he started with in terms of his relationship with the police.”

Ed Obayashi, a former special prosecutor and public defender who is a Plumas County sheriff’s deputy and instructor on use-of-force investigations, called Boudin’s decision “irresponsible.”

“There’s going to have to be a lot of explanation from the D.A. if something happens out there,” he said.

Randy Knox, a San Francisco defense attorney and former prosecutor, disagreed, saying “The easy thing for Boudin to do would be to prosecute Hampton.”

“I think the more thoughtful and deliberated thing to do is to gather as much information as possible before deciding how to proceed,” he said.

The new policy is only the latest move by the new district attorney drawing condemnation from the city’s rank-and-file, who work closely beside prosecutors in criminal matters.

Boudin last week made good on his campaign promise to not seek cash bail against any criminal defendants. Previously, he announced a diversion program for parents accused of crimes, pledged to stop charging gang enhancements and fired seven senior attorneys as he restructured his office less than a week after taking office.

“Just because he’s a left-wing, touchy-feely guy, to think he won’t use hard-nosed corporate management, that’s ridiculous,” said Dan Horowitz, a Lafayette defense attorney who supported Boudin’s election campaign. “Now he’s drawing another line in the sand.”

Whether or not the decision was part of a new policy, it still has not sat well with many in the department. Mayor London Breed and Chief Bill Scott each sent letters to every police officer in the department pledging their support for the officers.

“I have no doubt that this decision has created a great deal of confusion, frustration, and anger within the department,” Breed wrote in a message Monday obtained by The Chronicle. “I have spoken with the District Attorney and he made it clear that the investigation into all the circumstances and facts surrounding the incident must be resolved before any decision to file charges can occur to avoid any conflict of interest.”

The chief on Friday wrote to officers that “This unprovoked attack was a violent, criminal act. I want you to know that we remain committed to working with the DA to see that justice is done in this case for our officers.”

Montoya blasted the chief’s statement, saying Scott didn’t adequately stand up for the members. He was more happy with San Jose Police Chief Eddie Garcia’s reaction. He called Boudin’s decision “shocking and despicable” in a tweet Sunday, and added “I feel terrible for the courageous men and women of the SFPD.”

San Francisco Chronicle staff writer Carolyn Said contributed to this report.

Evan Sernoffsky is a San Francisco Chronicle staff writer. Email: esernoffsky@sfchronicle.com Twitter: @EvanSernoffsky