An investigation by federal prosecutors into the District’s crime lab raised questions about “integrity and competence” and revealed lapses in ballistics examinations, including some that lacked supporting documentation and an instance in which an analyst studying bullet fragments never removed them from a plastic bag.

The three-month inquiry by the U.S. attorney’s office and the FBI also uncovered concerns that managers with the D.C. Department of Forensic Sciences may have glossed over potential problems because of fears that prosecutors would blacklist analysts from testifying in court.

The unusual report, obtained by The Washington Post, was written by the office of the former U.S. attorney for the District, Jessie K. Liu, and dated Jan. 31, her last day as the city’s top law enforcement officer.

Liu wrote in a letter that the investigation, first reported last month by The Post, did not support criminal charges against agency employees or uncover any criminal cases that had been “adversely affected or compromised.” But she referred the findings to Daniel W. Lucas, the District’s inspector general, and asked his agency to look into “mismanagement, poor judgment, and failures of communication” within the forensics agency.

Prosecutors recommended that an inspector general inquiry consider the practices and standards involved in ballistics analysis as well as the agency’s “institutional grasp of the importance of integrity issues to its work,” according to the report.

The 33-page review uncovered tension between the U.S. attorney’s office and the Department of Forensic Sciences, agencies that must work together to build criminal cases. The city’s crime lab examines firearms, bullets, DNA and other evidence.

Prosecutors noted that one DFS response to their questions was “generally abstruse and defensive” and that the agency in November notified prosecutors of disciplinary matters that were “not previously disclosed.” They said the inquiry raised concerns about one manager’s “judgment and candor.”

In an interview, DFS Director Jenifer Smith said she disagreed with prosecutors’ concerns about the culture in the firearms unit. “That’s their opinion,” she said.

Smith defended her agency Thursday at a D.C. Council Judiciary and Public Safety Committee hearing. When council member Charles Allen (D-Ward 6), chairman of the committee, mentioned The Post’s initial story and asked about the status of the investigation, Smith said it had ended and that no charges had been filed.

“The investigation is closed, and no quality issues were identified,” Smith told Allen. “We are grateful that the investigation is over and we can move past it.”

Smith, who was copied on Liu’s letter, did not mention the concerns raised by prosecutors or note that they suggested a further inquiry by the city’s Office of the Inspector General.

In the hallway after the hearing, Smith said she “welcomed” an investigation by the city. “We are very transparent,” she said.

In a statement, Lucas did not say whether he would undertake the investigation, adding that his office regularly receives referrals, internally and externally. “Our job is to determine if there is any action to be taken by my Office,” Lucas said.

Liu’s letter and attached report have begun to affect court cases as they circulate among D.C. defense attorneys angered that information about the investigation was not provided to them sooner.

On Monday, D.C. Superior Court Judge Neal E. Kravitz dismissed a murder charge against a man named Keith Archie, who was about to face trial in a 2017 fatal stabbing.

With a jury seated and opening statements set to begin, prosecutors handed over information on the DFS investigation to the defense. Although Archie’s case does not involve a shooting, his lawyers wanted time to determine if the concerns by the U.S. attorney’s office may affect other aspects of the DFS, not just the firearms unit. Under Kravitz’s decision, prosecutors may refile the charges.

And late last week, defense attorney Evan Parke filed a motion asking two D.C. Superior Court judges to impose sanctions against the federal prosecutors and their supervisors handling cases against one of his clients. Parke said the government should have disclosed its concerns about the DFS before offering a plea deal in the cases, which included a felony burglary charge.

“I have asked prosecutors when they first learned of this issue. Their response was radio silence,” Parke said. “But someone’s freedom is on the line. People are going to jail. And the prosecution possibly isn’t being upfront about a key aspect of a deal that potentially sends someone to jail.”

Federal authorities began the probe last fall after a former firearms examiner told prosecutors about his concerns with the unit’s work. The inquiry centered on cases the department handled in 2017, during the seven months the former employee worked there.

The former employee told prosecutors that one firearms examiner, Steven Chase, had essentially forged the former employee’s signature on a case file, falsely indicating that he had verified Chase’s ballistics analysis when he had not. As part of the lab’s quality control, each examiner’s forensic conclusions are to be reviewed by a colleague to ensure that there are no errors.

The former worker told prosecutors that he wrote a detailed report about Chase’s actions to supervisors and that a manager told him to change the wording of his complaint to lessen the negative impact on Chase. The worker secretly recorded that conversation with the manager.

The former worker also alleged that some ballistics reports he had reviewed lacked specific documentation, leading him to question whether evidence was being thoroughly examined.

Over the following weeks, prosecutors in the fraud and public-corruption section and FBI officials interviewed dozens of employees and reviewed documents and emails.

Prosecutors said they ultimately were not able to conclude that Chase intended to enter false information in a case file. According to the report, Chase said he believed that the colleague had verified the work and simply had not signed off on it. The former employee said he eventually did review Chase’s work in the case and found it to be sound.

And while investigators found the former employee’s intentions to be “sincere,” they also described him as “an ineffective communicator — raising the question of whether his difficulty crystallizing and articulating concerns could have contributed to a miscommunication within DFS.”

The prosecutors also determined that the claim that analysts were not thoroughly inspecting evidence was not completely accurate. Prosecutors wrote that although an analyst may not have followed all DFS protocols, the final results were not erroneous. The analyst in question is no longer a lab employee. In one of those instances, the same analyst examined bullet fragments without removing them from a clear plastic bag. This was a violation of DFS practices, the report said.

During her testimony last week, Smith told Allen that the investigation was based on “unfounded allegations” and that any issues had been addressed in 2017, when it was discovered that an examiner had made a mistake on two cases and that two other examiners confirmed the erroneous findings. At that time, the agency restructured its firearms evaluation processes and reviewed 150 firearms examinations, fixing the issues the former employee had raised with prosecutors, she said.

But prosecutors wrote that while their investigation did not find any criminal conduct, they uncovered other concerns that prompted them to refer the case to the inspector general.

One employee who also has since left the agency told investigators that she “felt pressured by Smith” to not use too much detailed information regarding disciplinary issues, to avoid having prosecutors identify an analyst as someone whose work or credibility may be in question. In such instances, prosecutors may have to turn over that information to defense attorneys, who could then use it to challenge the findings.

That same employee, however, also told the investigators that she did not find Smith’s request to be “unethical” and that she could not think of an example of Smith pressuring her to make changes to analysts’ disciplinary reports.

In an interview after the Allen committee hearing, Smith denied that there was ever a decision by managers to withhold negative reviews of examiners. “That has never been the case,” she said.