WASHINGTON — More than 3,000 inmates were freed from federal prison on Friday as part of the Justice Department’s implementation of the sweeping bipartisan criminal justice overhaul that President Trump signed into law late last year.

The department has faced sharp criticism over its execution of the act. The partial government shutdown in January stymied progress on its implementation, which was further overshadowed by a debate over when the bill authorized the release of thousands of prisoners.

Advocates have expressed worries that the department would slow-walk implementation because former Attorney General Jeff Sessions and others within the department who stayed on after he was fired had fiercely opposed the law.

The deputy attorney general, Jeffrey A. Rosen, sought to tamp down those concerns at a news conference on Friday to announce that the department had met the deadline for the prison releases, as well as other milestones of the law, called the First Step Act.

“The timely, efficient and effective implementation of the First Step Act is a priority for the Department of Justice and this administration,” Mr. Rosen said. “The department intends to implement this law fully and on time.”

In addition to the release of 3,100 inmates, the Justice Department said that it had redirected $75 million from Bureau of Prisons inmate care programs and institutional administrative funding to fully fund the law for the fiscal year that started in October.

The department will work with Congress to obtain the funds needed for the law going forward, Mr. Rosen said, including money for services at its heart, such as vocational and job readiness training, rehabilitation and trauma care services that prisoners can participate in to earn reduced sentences.

He also said that the department had created a tool that gauges whether inmates are ready to leave prison. The Bureau of Prisons will use the tool to screen all federal inmates to identify risk factors that could increase their likelihood of recidivism, and match them with programs aimed at reducing that risk, such as drug treatment and job training courses.

As the law is written, inmates who had already earned credits and were eligible for early release could not leave until after the Justice Department created the risk assessment tool. Critics argued in recent months that the language did not accurately reflect the intent of the lawmakers who drafted the bill, and they pressed Congress to rewrite it so that thousands of prisoners could immediately be freed.

That didn’t happen, so the eligible prisoners had to wait until Friday for early release. Of the 3,100 prisoners released nationwide, about a third of them were subject to detainers, meaning they will go from federal custody to serve state prison sentences or they are in the United States illegally and will be released to face immigration court proceedings.

Amid acrimony between Democrats and Republicans, the criminal justice overhaul passed overwhelmingly in December. Mr. Trump has hosted two events to highlight the law, and he is likely to tout it during his re-election campaign as one of his administration’s signature achievements.

But the overhaul had a difficult birth, partly because of opposition from Mr. Sessions, according to legislative aides and advocates who worked on it. Mr. Sessions promised to provide feedback, they said, but he eventually criticized a draft without giving lawmakers what they considered substantive recommendations or improvements.

A representative for Mr. Sessions, who has returned to private life, disputed that characterization Friday in a statement. “The Department provided significant substantive feedback on the proposed bill over several month period both at the staff and member level,” the statement said, adding, “The members also were well aware of the Department’s grave concerns about the bill’s large reductions in sentences for violent and serious federal criminals and the need to maintain truth in sentencing.”

Mr. Sessions was opposed to retroactively reducing sentences for drug offenders, according to a former administration official familiar with the deliberations who spoke on condition of anonymity because he wasn’t authorized to share details. Mr. Sessions also opposed sentence reductions for repeat offenders, believing that repeat criminal behavior increased the likelihood of recidivism.

Once it was clear that Mr. Trump supported the bill, Mr. Sessions began publicly backing it but privately worked through back channels to oppose it, encouraging law enforcement associations and other groups to voice their opposition to lawmakers and other stakeholders. When supporters of the bill heard about his efforts, they sought White House help to ensure its passage.

But after Congress passed the law, they expressed concern that Justice Department officials who had sided with Mr. Sessions and remained in their jobs after he was fired in November would delay its implementation.

“Sessions represented an all-time low for prospects for successful passage at the time and also prospects for implementation,” said Holly Harris, the president of Justice Action Network, a criminal justice reform advocacy group. “We’re looking at a vastly improved situation,” she said of Attorney General William P. Barr, who replaced Mr. Sessions in February.

Mr. Barr assured supporters of the law that he would back its full implementation. Ahead of his confirmation hearing, he met with senators including Charles E. Grassley, Republican of Iowa and the former head of the Senate Judiciary Committee, who was one of the bill’s strongest backers. Mr. Barr said that his thinking on criminal justice had evolved, and that he no longer supported the harsh sentencing measures that he had pushed for during his first stint as attorney general in the early 1990s.

During an interview this month after touring a federal prison in Edgefield, S.C., Mr. Barr defended the tough-on-crime measures he had supported at the time as “essential for reducing the crime rate and also tackling the crack epidemic.” But with crime rates down substantially, he said he felt that the time was right to identify and free inmates who no longer constituted a safety risk.

“After someone has been in prison for a substantial period of time, and you can really assess whether they continue to pose a threat to the community,” Mr. Barr said, “then obviously you’re more inclined to modify the sentence or strike the balance in favor of some kind of monitoring that doesn’t involve the heavy cost and the isolation of this kind of prison system.”

The law consists of a package of incentives and new programs designed to improve prison conditions and prepare prisoners considered low risks for recidivism to re-enter society. It also outlawed the shackling of pregnant inmates and the placement of juveniles in solitary confinement and said the Bureau of Prisons must place prisoners close to home if possible.

The law also makes retroactive the 2010 Fair Sentencing Act, which decreased the relative penalty for possession of crack versus powder cocaine.

In the run-up to Friday’s announcement, both Mr. Barr and Mr. Rosen worked with Antoinette Bacon, a Justice Department lawyer who is in charge of implementation, to ensure that the department met the deadline for developing the risk assessment tool, called Pattern, and prisoner releases.

In June, Mr. Rosen met for nearly two hours with the team creating Pattern, discussing research that showed how risk factors including age and gender affected the likelihood of recidivism. Ignoring these disparities, the committee warned, could result in early releases being applied unfairly.

Mr. Barr met with the committee on Thursday to hear about steps to improve Pattern in the coming months as the committee gets feedback from the Bureau of Prisons and advocates about its effectiveness.

In addition to Mr. Barr’s recent visit to the medium-security federal prison in South Carolina, Mr. Rosen visited a maximum-security penitentiary in Colorado in recent weeks to discuss programming and rehabilitation efforts.

Advocates said they were pleased that Mr. Barr was speaking positively about the criminal justice overhaul, but they called for a congressional oversight hearing about the implementation of the entire law and vowed to closely monitor the process, especially the efficacy of the risk assessment tool.

It “has been a real mystery to a lot of groups,” said Ms. Harris.

Katie Benner covers the Justice Department. She was part of a team that won a Pulitzer Prize in 2018 for public service for reporting on workplace sexual harassment issues. @ktbenner

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