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Jeffrey Epstein's apparent suicide in a New York jail followed steep and persistent staffing shortages that exceeded the rate of decline in the federal prison population, according to an analysis by the Marshall Project.

The numbers tell the story: The analysis found that the federal prison system lost 12 percent of its workforce from the start of the Trump administration through the end of 2018. Administration officials have argued that the staff drop, which resulted partly from a hiring freeze, was mitigated by a reduction in the number of federal prisoners. But the drop in Bureau of Prisons (BOP) staff was nearly double the rate of decline in the prison population overall, the analysis found.

Over a two-year period between Sept. 2016 and Sept. 2018, the bureau lost 10 percent of its employees. In that same period, the total number of federal prisoners dropped by just over 5 percent.

Epstein, a wealthy financier, was being held in a Manhattan Correctional Center jail cell on federal charges of operating a child sex trafficking ring when he was found dead Saturday. Of the two guards assigned to monitor Epstein's cell area, one was not a full time correctional officer but a substitute, the New York Times reported. Both guards were working overtime—one for four or more days, according to the American Federation of Government Employees, the union for federal corrections officers.

Attorney General William Barr lifted the hiring freeze in April, and sweeping federal reforms and sentencing guideline revisions have continued to clear out prison cells and shorten prison time for thousands of people convicted of drug crimes, partly lessening the need for new correctional officers. But the hiring freeze, and the retirement of many prison employees who entered during a hiring boom in the 1990s, diminished staff to a point where prison teachers, nurses, and chaplains continue to be asked regularly to fill in on guard duties—a so-called "augmentation" that is facing renewed criticism from some employees and union representatives.

On Tuesday, the Bureau of Prisons, at Barr's direction, transferred the Metropolitan Correctional Center's warden to the Northeast Regional Office pending the outcome of FBI and DOJ Inspector General investigations. Two staff members assigned to the unit Epstein was housed in have been placed on administrative leave, Justice Department spokesperson Kerri Kupec said in a statement.

Barr has cited "serious irregularities" at the jail, and he pledged a thorough investigation.

Union members and prisoner advocacy groups say that intense scrutiny should expand to the attorney general and the White House, who have left the Bureau of Prisons short-staffed and without a director for several months.

A staffer with more than 14 years of experience in federal prisons and who is not a correctional officer said teachers and medical staff are among those at his institution being called upon to fill in on prison guard shifts under "augmentation."

"It puts staff at risk," said the prison employee, who asked not to be named because he was not authorized to speak publicly about the practice. He noted he has seen some teachers spend half their time working guard shifts.

But one expert said augmentation is not a new practice. Gerard Bryant, who retired in 2014 as associate warden of the Metropolitan Detention Center in Brooklyn after more than two decades with the Bureau of Prisons, said all prison employees have always known they might be called upon to fill in occasionally on guard shifts. Nearly all prison employees go through the same three-week training as corrections officers and are also licensed to use firearms, Bryant said.

"The bottom line is: People are hired in BOP prisons with the understanding that you are correctional workers first," said Bryant, now director of the Counseling Services Center at John Jay College, where he teaches and researches prison management.

However, Bryant noted that a wave of retirements is exacerbating staffing problems at federal prisons. "It's not that the BOP does not want to fill positions, they cannot fill the positions quickly enough," he added.

Union officials said guard duties have never been augmented at the rate they have in recent years. They blame mostly the hiring freeze under the Trump administration.

From January 2017, when President Trump took office, to the end of 2018, the Bureau of Prisons’ staffing numbers dropped by more than 4,600 people—12 percent of its total staff—including correctional officers, psychologists, administrators, or anyone else who works in the prisons, according to data from the Bureau of Labor Statistics. In April, Barr acknowledged in a congressional hearing that the hiring freeze led to understaffing. He said by that point the prison system was down by as many as 5,000 employees. Union officials contend the number of positions left open by attrition grew to as many as 6,000.

"I think this is an area where we have stumbled," Barr told lawmakers.

Don Drewett, legislative coordinator for the American Federation of Government Employees' Council of Prison Locals, said he was disappointed by comments this week blaming overworked corrections officers and supervisors for Epstein's inadequate supervision. He said Barr should know four months without the freeze is not enough time to make up for widespread officer shortages.

"It's not like a light switch. When you're down 6,000 people, you just can't turn the switch and make up for years of positions left open," Drewett said. "This is kind of like you're playing this game of chicken, and eventually something bad happens, and shit rolls downhill, and this is classic Justice Department that says, 'Hey, this shouldn't have happened.'"

The Justice Department and federal prison officials did not respond to requests for comment.

The Bureau of Prison's vacancies extend all the way to the top. The bureau has operated without a permanent director for several months, the agency's second long stretch without a permanent leader in four years. The Obama administration failed to name a prisons director after the retirement of Charles E. Samuels in 2016.

Nearly two years had passed before the Justice Department appointed former military corrections officer Mark Inch as director in late 2017. Eight months later, Inch resigned, citing "matters of conscience" in carrying out duties under then-Attorney General Jeff Sessions. Inch's post has gone unfilled since May of 2018. Union officials say the lack of leadership has sunk morale, delayed long-term planning, and allowed the DOJ to overlook the safety needs and staffing concerns of federal prisoners and corrections officers.

“Clusterfuck doesn't begin to describe the current state of the BOP, and it dates far beyond the Trump administration," said David Safavian, deputy director of the American Conservative Union Foundation's criminal justice reform center, who has worked with the White House this year to create programs that help prisoners find jobs upon release. "Anyone who thinks BOP is a high performing organization has never been inside a federal prison. The Epstein fiasco underscores the staffing, morale, and healthcare challenges facing the Justice Department. And it now puts a spotlight on the lack of permanent leadership at BOP."

Union officials are also critical. Without the input from an appointed director, "the administration continues, year after year, to put forth budget proposals that would further underfund BOP and exacerbate the strains we're already seeing," said Eric Young, president of the Council of Prison Locals.

This year, the DOJ's budget plans included a reduction of 1,168 positions at the Bureau of Prisons to "adjust the inmate to staff ratio at the BOP's institutions in light of the declining inmate population."

Holly Harris, executive director of the U.S. Justice Action Network, a group that advocates for changes to improve the prison system, said the Bureau of Prisons' leadership void gives the Justice Department full control to steer it in directions that have run counter to the will of Congress and even the White House, particularly when it comes to easing criminal punishment. Barr this week blasted local prosecutors who "style themselves as 'social justice' reformers," while his predecessor, Sessions, opposed the First Step Act. The federal law Trump signed last year decreased some drug sentence lengths, expanded time-off for good behavior, and created more in-prison job skills training. It has led to early releases of at least 3,000 federal prisoners, most of whom were set free after the BOP hiring freeze was lifted.

"Clearly there is a lack of oversight, and it's going to have to get addressed at some point," Harris said. "But I'm as skeptical as anyone else that it's going to happen."

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