Federal authorities arrested nine current and former Boston police officers Wednesday and charged them with running an overtime scam out of the department’s evidence warehouse, where they allegedly falsified time sheets to collect more than $200,000 over a three-year period.

The officers, including a lieutenant and two officers still in the department, are accused of claiming they had worked full overtime shifts to clear an evidence backlog, when they worked only a portion of that time. Authorities alleged that three of them were supervisors who not only took part in the scam, but approved the false reports, according to a federal indictment unsealed Wednesday.

The officers also allegedly inflated the time it took for them to transport surplus items, such as prescription drugs confiscated by police, to an incinerator in Saugus for destruction.

“These officers are charged with stealing taxpayer money, year after year, through fraud,’’ US Attorney Andrew E. Lelling said in a statement. “Beyond the theft of funds, this kind of official misconduct also erodes trust in public institutions, at a time when that trust is most needed.’’

The indictment comes amid a national reckoning over systemic abuses within law enforcement and amid widespread calls for police reform. Several departments across the state have been mired in payroll scandals in recent years, most notably the Massachusetts State Police, which had about 50 troopers implicated and nine guilty pleas in federal court. But the Boston Police Department, the venerated, and oldest, police force in the country, had emerged unscathed, until now.

Each of the officers was arrested at their homes Wednesday morning without incident. They appeared later that afternoon in a video court hearing at the federal courthouse in South Boston and were released from custody on their own recognizance shortly later. The officers, who each collected between $16,000 and $42,000 in alleged fraudulent overtime pay over the three-year scam, face up to 10 years in prison on charges including conspiracy to commit theft, and embezzlement, aiding and abetting, authorities said.

Three current members of the department, Lieutenant Timothy Torigian, 54; Michael Murphy, 60; and Kendra Conway, 49, have been suspended without pay pending the prosecution, according to the Police Department.

The other six officers implicated in the scheme had retired over the last 18 months amid the investigation. They are Sergeant Gerard O’Brien, 62; Sergeant Robert Twitchell, 58; Henry Doherty, 61; Diana Lopez, 58; James Carnes, 57; and Ronald Nelson, 60.

“The allegations and behavior alleged in today’s indictments is very troubling and in no way reflect the attitudes of the hard-working employees of the Boston Police Department,’’ Police Commissioner William Gross said in a statement. “I hold my officers to the highest standards and expect them to obey all the laws that they have taken an oath to uphold.’’

Gross said the department’s anticorruption unit discovered the payroll abuses within the evidence management unit, though he would not describe the nature or the origins of the investigation, or whether any other officers were involved. The criminal investigation was ultimately handled by federal investigators.

Suffolk District Attorney Rachael Rollins, who watched the virtual court hearings Wednesday, said she was dismayed by the allegations. Rollins’s office said the nine officers’ credibility has been tainted: Their names have been added to a database maintained by her office that raises flags whenever their names are associated with a criminal case the office is pursuing.

“We in law enforcement cannot adequately perform our duties if the community does not trust us or believes that we lack integrity,’’ she said in a statement.

Mayor Martin J. Walsh called the allegations “an affront to the thousands of police officers who do their jobs every day with honesty, integrity, and bravery.

“I am outraged and, quite frankly, outright disgusted at the utter breach of trust by these nine individuals at the Boston Police Department,’’ Walsh said.

The indictment alleged that the Boston police officers worked together in their conspiracy. The group was responsible for caring for and cataloging evidence at the department’s warehouse in Hyde Park. As part of those duties, the officers were allowed to work overtime – at one-and-a-half times their pay – in four-hour weekday shifts.

For years, the officers allegedly claimed to work a full overtime shift, but left in many cases two hours early. Alarms at the warehouse signaled their departures. The supervisors, Torigian, O’Brien, and Twitchell, approved the fraudulent work slips and also forged their own, according to prosecutors.

Authorities said the scam ran from 2016 to early 2019, when several of the officers were placed on administrative leave.

Torigian, the highest ranking officer, made the most — close to $43,000 in fraudulent overtime — during the three-year scam, according to the indictment. Several of the other officers made more than $25,000.

His lawyer, Robert Goldstein, said the amount of money allegedly stolen over three years concerns “a tiny sliver of the overall time Tim has dedicated to the citizens of Boston over the course of a 30-plus-year career, but they are nonetheless very serious, and we look forward to proving the government wrong.’’

“We fully expect Tim will be exonerated in this matter and look forward to pursuing a speedy trial in that pursuit,’’ Goldstein said.

The figures do not represent the total amount of pay the officers collected, including tens of thousands of dollars in other overtime. In 2018 alone, the nine officers collectively earned $1.64 million in pay, including $373,716 in overtime.

David Meier, an attorney for O’Brien, called his client a dedicated police officer of more than 30 years, saying the charges involve $25,000 “at the tail end of an otherwise honorable career in law enforcement.’’

“These are the types of allegations of overtime abuse that are traditionally addressed and fairly and appropriately resolved by the Boston Police Department and state and law enforcement officials,’’ he said. “We look forward to defending against these federal charges in court.’’

Several of the other defendants have lengthy careers with the department. One of them, Twitchell, was featured in “Boston’s Finest,’’ a reality television series that was produced by Dorchester native Donnie Wahlberg.

The case could raise questions about the police department’s management of its resources.

City Councilor Andrea Campbell, who has probed police spending and called for greater oversight and accountability within the department, said the department spends tens of millions of dollars on police overtime that could fund community-lead violence prevention efforts, “but instead was possibly partly spent on the fraudulent claims of these officers.’’

“The city of Boston needs to adopt real strategies to provide oversight and accountability for all departments, and get serious about reducing and reallocating police overtime spending,’’ she said.

Travis Andersen and John R. Ellement of the Globe staff contributed to this report.