President Obama visits the El Reno Federal Correctional Institution outside Oklahoma City in July 2015. (Kevin Lamarque/Reuters)

One recent afternoon, President Obama sat down for lunch with seven former prisoners at the Washington restaurant and bookstore Busboys and Poets. He had just commuted the sentences of 61 inmates and was listening to the stories of other ex-offenders who had been granted clemency.

Obama was clearly moved by what he heard.

“It does not make sense for a nonviolent drug offender to be getting 20 years, 30 years, in some cases life, in prison,” Obama said at the lunch. “That’s not serving anybody.”

In the waning months of his presidency, Obama has made commutations for nonviolent drug offenders a centerpiece of his effort to reform the country’s criminal-justice system.

But behind the scenes, the administration’s highly touted clemency initiative has been mired in conflict and held up by a bureaucratic process that has been slow to move prisoner petitions to the president’s desk.

Obama has granted 306 commutations to federal prisoners — more than the past six presidents combined. But as of Friday, 9,115 commutation petitions were pending with little time left to review them. Of these, fewer than 2,000 appear to be eligible for the president’s clemency program, according to a Justice Department official. Thousands more are still being reviewed by outside lawyers.

From the beginning, the program was beset by problems, including a lack of resources and a cumbersome, multilevel review system. The U.S. pardon attorney at the Justice Department makes recommendations that move to the deputy attorney general, who reviews the cases and sends them to the White House counsel, who considers them again before choosing which ones go to Obama.

The pardon attorney became so frustrated that she quit earlier this year and wrote a scathing resignation letter to Deputy Attorney General Sally Q. Yates. Deborah Leff said that despite her “intense efforts” to do her job, the Justice Department had “not fulfilled its commitment to provide the resources necessary for my office to make timely and thoughtful recommendations on clemency to the president.”

“The position in which my office has been placed, asking us to address the petitions of nearly 10,000 individuals with so few attorneys and support staff, means that the requests of thousands of petitioners seeking justice will lie unheard,” Leff wrote.

On Thursday, Obama commuted the sentences of 58 prisoners, his second round of clemencies in three months as the program has picked up steam. Administration officials say that they are addressing obstacles that have plagued the clemency initiative. The Justice Department has added lawyers to the pardon office. And White House Counsel Neil Eggleston has promised that many more petitions will be granted in the president’s final eight months.

“The President is deeply committed to the clemency initiative. That is evident not only by the historic number of commutations he’s granted to date, but by his wholesale approach to revamping the way the government approaches commutations,” White House spokeswoman Brandi Hoffine said in a statement. “That change helped spark a long overdue conversation about reforming our criminal justice system, which we hope will result in Congressional action so that many more deserving individuals can benefit from a second chance.”

Problems from the start

In April 2014, Deputy Attorney General James Cole announced the administration’s clemency initiative and a new pardon attorney, Leff, a former civil rights lawyer and acting head of the Justice Department’s legal aid program, the Access to Justice initiative.

Cole said he would “be personally involved in ensuring the pardon attorney’s office has the resources needed to make timely and effective recommendations to the president.”

But attorneys who have worked with the Justice Department said there were never enough lawyers and support staffers to make the program work. Leff’s office had 10 attorneys fielding thousands of petitions.

Under criteria set out by then-Attorney General Eric H. Holder Jr., low-level drug offenders are eligible for clemency if they have been in prison for at least 10 years; had no significant criminal history; have no connection to gangs, cartels or organized crime; have demonstrated good conduct in prison; and probably would receive a “substantially lower sentence” if convicted of the same offense today.

An attorney who worked in the pardon office at the same time as Leff said that with petitions flooding in, it was extremely difficult with so few lawyers to sort out complicated drug cases and figure out whether they met the department’s strict criteria.

To get more help, Cole reached out to the private bar to set up another layer of lawyers to read applications.

Outside lawyers formed an organization called Clemency Project 2014, which includes Families Against Mandatory Minimums, the American Civil Liberties Union, the American Bar Association and the National Association of Criminal Defense Lawyers.

An army of about 4,000 volunteer lawyers from across the country signed up to help in what has become one of the largest pro bono efforts in the history of the American legal profession. Seventy large law firms, more than 500 small firms and solo practitioners, and 30 law schools are involved, according to Cynthia W. Roseberry, the project’s manager.

But it took nearly a year for the group to get organized and recruit and train lawyers, many of whom had no experience in criminal law.

An overwhelming 36,000 inmates — about 17 percent of the federal prison population — filled out surveys asking for help from the Clemency Project.

Even though the Justice Department had its own backlog, officials there privately complained that the outside Clemency Project lawyers, with their multiple levels of review, were taking too long to send more petitions.

That in turn frustrated the Clemency Project attorneys, who said they were working carefully to locate old legal documents, contact prosecutors and judges, look at prison behavior records and try to get pre-sentencing reports and sentencing transcripts. At the same time, they have been weighing risks to public safety.

“It’s going to be really surprising if none of these people ­re-offend, and no one wants to be the person who said yes to the one person who re-offends in however many years,” said one lawyer reviewing clemency applications who spoke on the condition of anonymity because of the sensitive nature of case deliberations.

Turnover at Justice Dept.

Meanwhile, Cole and Holder — the two men who had launched the clemency initiative — left the Justice Department in 2015.

Yates, the career prosecutor and former U.S. attorney who became the new deputy attorney general, took over the supervision of clemency petitions.

Over time, pardon attorney Leff’s frustrations grew.

Leff said Yates reversed many of her decisions and would not allow her to have any contact with the White House counsel.

After 20 months, Leff abruptly resigned.

“I have been deeply troubled by the decision to deny the Pardon Attorney all access to the Office of the White House Counsel, even to share the reasons for our determinations in the increasing number of cases where you have reversed our recommendations,” Leff wrote in her resignation letter to Yates, which was first reported by USA Today.

A Justice Department lawyer who worked with Leff said the pardon attorneys in prior administrations talked directly to the White House counsel to explain their recommendations.

When she left, Leff released a statement saying that she has known Obama for more than 20 years: “His commitment to reinvigorating the clemency process — and the promise that holds for justice — can change the lives of a great many deserving people.”

Leff implied that Obama’s clemency program was being thwarted by the Justice Department’s process. “It is essential that this groundbreaking effort move ahead expeditiously and expand,” she said.

When asked by a reporter last month about the roadblocks Leff said she had faced, White House press secretary Josh Earnest replied: “I think there were a couple of concerns that she raised, and some of them were not inconsistent with concerns that we’ve had. The first is, we would like to see that unit of the Department of Justice be given more resources to do their work. And in the president’s latest budget proposal, there’s a significant increase proposed for the budget of that office.”

Some critics say the White House could have avoided many of these headaches by modeling the process after the way President Gerald Ford handled clemencies for Americans who had deserted the Army or failed to show up for the draft during the Vietnam War. With 600 people working on a special commission to review the cases, Ford granted 14,000 clemencies in one year.

Law professor Mark Osler, co-founder of New York University’s Clemency Resource Center, said the initiative also might have gone more smoothly if Obama had moved the pardon attorney’s office into the White House rather than keeping it under career prosecutors who may find it difficult to reverse other prosecutors’ decisions.

With Leff gone, in February the Justice Department named a new acting pardon attorney, longtime federal prosecutor Robert A. Zauzmer, who vowed to look at each of the thousands of petitions and “make sure an appropriate recommendation is made to the president.”

The Justice Department has given Zauzmer more resources — 10 additional prosecutors across the country have been detailed to work remotely with his office. Department officials are also allowing Zauzmer to have contact with the White House counsel.

“The Justice Department has dedicated the maximum amount of resources allowed by Congress to the Office of the Pardon Attorney, and we have requested additional funds from Congress for each year the initiative has been in place,” Justice Department spokeswoman Emily Pierce said in a statement.

Principal Associate Deputy Attorney General Matthew Axelrod said Yates “is so passionate about clemency.”

“She takes a grocery bag of petitions home and spends her weekends reading them,” Axelrod said. “There’s no one who’s more committed.”

Yates has put more pressure on the Clemency Project to speed up its work. Last week, she sent a letter to the volunteer attorneys saying, “Time is of the essence and the inmates who raised their hands for your assistance still need your help.”

James E. Felman, a lawyer and one of the leaders of the Clemency Project who visited prisons to help find inmates who meet the criteria, said the process is more streamlined. The coalition is sending batches of petitions to the pardon attorney twice a week and has sent 950 petitions in all. There are still about 8,000 left to finish reviewing. “Time is running out, and if we don’t get these petitions filed soon, there is no way that this president is going to ever see them,” Felman said.