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Perhaps the most far-reaching idea was to reclassify the more than 40,000 Border Patrol agents and customs officers as “national security employees,” just as all FBI agents and employees at a number of other Homeland Security agencies currently are. Taking away their status as civil servants, the thinking went, would make it easier to fire corrupt and abusive employees.

It was, to be sure, an extreme measure. But the panel, a subcommittee of a larger Homeland Security advisory council, had been created late in President Barack Obama’s second term because U.S. Customs and Border Protection seemed in crisis, and the panel subsequently determined that the agency was plagued by a system that allowed bad actors to stay on the payroll for years after they’d engaged in egregious, even criminal, misconduct. Because of civil service protections, a Border Patrol agent who’d been disciplined for bad behavior could challenge his or her punishment through four rounds of escalating appeals before taking the case to an arbitrator or a federal hearing board.

And the panel — headed by William Bratton, who had run police departments in Boston, New York City and Los Angeles — was deeply concerned about the persistent strain of lawlessness among CBP employees. In a preliminary 2015 report, the panel had noted that “arrests for corruption of CBP personnel far exceed, on a per capita basis, such arrests at other federal law enforcement agencies.” CBP, the panel’s members concluded, was “vulnerable to corruption that threatens its effectiveness and national security.”

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The civil service idea, it turned out, was dead on arrival, one of any number of the panel’s recommendations that have failed to materialize. At least nine of the panel’s suggested reforms, first put forward more than three years ago, have been dropped or haven’t yet been fully put into practice, according to a CBP spokesperson. CBP officials rejected taking away civil service protections in part because it would anger the union representing Border Patrol agents.

“That was going to be a difficult one,” recalled R. Gil Kerlikowske, who served as CBP commissioner at the time of the panel’s reports on corruption and misconduct in 2015 and 2016.

The union did not respond to requests for comment.

CBP, and chiefly the Border Patrol, is again front and center as the nation confronts the volatile issue of illegal immigration. The administration of President Donald Trump has pledged to take the “handcuffs off” law enforcement agents as part of an aggressive push to stem the flow of migrants across the country’s southern border. The performance of Border Patrol agents was one element of the widespread outrage provoked by the administration’s decision to separate children from their parents at the border.

The agency, at least publicly, agreed with many of the advisory council’s recommendations when they were issued in 2016. And last year, Kevin McAleenan — then head of CBP and recently named by Trump to be the acting secretary for Homeland Security — told Congress that the agency had implemented 42 of the panel’s 53 recommendations.

A closer look, however, indicates that CBP has moved slowly on several central reform proposals. To cite one: The panel encouraged CBP to create a discipline czar, a high-level official who could track all the misconduct and corruption cases and keep the agency’s commissioner informed about them.

In a statement to ProPublica, CBP said the agency, more than three years later, was still “working on the best options to meet this recommendation.”

Perhaps most significant: The panel recommended that CBP hire 350 internal affairs investigators over a three-year period and task them with looking into misconduct and corruption. So far, the agency has brought on only about 50 investigators.

Some experts on immigration and border protection fear that the prospects for lengthy and lasting reforms of CBP have dimmed under the current administration.

“They’re dragging their feet,” said Vicki Gaubeca, director of the Southern Border Communities Coalition, an advocacy group focused on holding CBP accountable. “What’s the motivation behind this taking so long?”

Looking at his former agency, Kerlikowske said he was more optimistic about the progress CBP has made, noting that some key reform proposals had been enacted and are still in effect. “I think it’s trending in the right direction.”

CBP is a relatively new creation. It was formed in the aftermath of 9/11, in 2003, when federal officials took two distinct organizations — the U.S. Customs Service and the Border Patrol — and fused them into a single agency operating beneath the umbrella of the Department of Homeland Security. (Several smaller agencies were also part of this reorganization.) It is now the nation’s largest law enforcement agency, a behemoth far larger, in both budgetary terms and personnel numbers, than either the FBI or the Drug Enforcement Administration.

Over the past 16 years, CBP employees have earned a reputation for both heroism and misconduct. Working under challenging conditions, they have disrupted dangerous smuggling rings and saved the lives of desperate migrants stranded in the scorching deserts of the American Southwest. But customs officers and Border Patrol agents have also run afoul of the law, often in extreme fashion. Every year, approximately 250 CBP employees are arrested, many on suspicion of serious felonies; dozens have been jailed in recent years on corruption charges, including weapons trafficking and collaborating with Mexican drug cartels.

During the Obama years, critics decried a series of incidents in which Border Patrol agents shot civilians, many of them Mexican nationals, often under questionable circumstances.

“It was a critical issue,” said Kerlikowske, who headed the agency at the time. “The Border Patrol was under a huge amount of scrutiny from the advocacy groups and the press.”

Kerlikowske and his deputies dramatically changed the agency’s policies around using firearms, bringing them in line with those of other law enforcement organizations. Shootings dropped precipitously.

Read More Over 200 Allegations of Abuse of Migrant Children; 1 Case of Homeland Security Disciplining Someone A federal judge found the department’s own records disturbing and ordered the names of the accused agents made public. Now, DHS has taken its fight against doing so to the 9th U.S. Circuit Court of Appeals.

But complaints of physical and verbal abuse by migrants taken into custody have not. According to a CBP document, each year the agency “receives and reviews hundreds of allegations” of excessive force. This year, CBP paid $125,000 to settle a lawsuit alleging that a Border Patrol agent groped the breasts and genitals of two teenage Guatemalan girls detained in Presidio, Texas. It’s unclear whether the agent at the center of the allegations has been disciplined or ousted from the patrol.

It was this sort of toxic behavior that Bratton and the other members of the advisory panel named by Obama were looking to address. Their assessment of CBP was stinging — the agency’s “discipline system is broken,” they wrote — and their recommendations were extensive, covering everything from the use of real-time GPS tracking to the deployment of body cameras.

Investigations into misconduct and criminality within the agency are handled by a host of different units with overlapping jurisdiction: local CBP supervisors; CBP’s nationwide internal affairs unit; the Homeland Security Department’s inspector general; the civil rights office at Homeland Security; and, in certain cases, the FBI and U.S. Department of Justice. The situation has led to bureaucratic turf battles and a general inefficiency, experts said.

The panel encouraged the two key players, CBP and the inspector general, to draft a formal memorandum of understanding laying out which cases would be investigated by the inspector general’s staff and which would be examined by CBP’s internal affairs investigators.

Three years later, the two sides have been unable to come to an agreement.

A CBP spokesperson blamed the impasse on the inspector general, who gets first crack at most misconduct investigations, saying the office “does not want to relinquish its first right of refusal.”

The inspector general’s office said it has a “productive working relationship” with CBP and its internal affairs unit. But the office believes that it, not CBP, should “investigate the most egregious allegations” of misconduct and that the inspector general’s staff should get the first look at those cases.

This week, the office issued a withering 69-page audit on disciplinary practices across the Department of Homeland Security, including CBP. According to the report, the department “does not have sufficient policies and procedures to address employee misconduct.”

CBP came in for particular scrutiny. Auditors surveyed more than 4,000 supervisors with the agency. Of those surveyed, 58% said they needed more training in responding to bad behavior by employees and taking disciplinary action. Thousands of lower-ranking employees who were surveyed expressed little faith in their bosses, with nearly a quarter saying that they feared retaliation for reporting misconduct by their colleagues, and more than 32% stating that they didn’t trust their supervisors to “take appropriate action to correct misconduct in the workplace.” Nearly 47% said they'd personally witnessed four or more acts of misconduct at CBP over the past three years.

The inspector general’s office has had its own embarrassments of late. This month, Acting Inspector General John V. Kelly resigned after the publication of damning media stories suggesting that he had improperly edited and revised the office’s reports on disaster relief efforts. Kelly insisted at the time that he had merely retired, although he said he had failed to set a tone of objectivity for his staff.

Few experts and advocates interviewed by ProPublica expressed faith in the CBP’s fragmented oversight system. They described it as a black hole, a vortex in which serious complaints are ignored or lost, simple investigations drag on for years, and victims are barred from learning whether the government employees who’ve harmed them have been sanctioned in any way.

“A multibillion-dollar federal agency shouldn’t work that way,” said Jeremy Slack, an assistant geography professor at the University of Texas at El Paso who studies migration patterns and law enforcement. The agency, he argued, has become secretive to a fault. “They’re not exactly open. A lot of the insight that I have comes from people who work at CBP and are afraid to go on the record.”

CBP said it is barred by federal privacy laws from disclosing the names of officers and agents sanctioned for misconduct. “However, to promote accountability and transparency, CBP does publish an annual discipline report containing aggregate discipline data,” said a spokesperson. The report tallies the number and types of misconduct investigations across the agency, but it does not detail the outcomes of individual cases.

Based in Nogales, Arizona, a small, dusty town in the Sonoran Desert, Joanna Williams works for the Kino Border Initiative, a Catholic group that aides migrants. She has frequent contact with federal officials.

In her experience, allegations of misconduct are frequently dealt with at the local level by supervisors, rather than professional investigators at any of the bodies tasked with overseeing CBP. In Williams’ estimation, the number of cases handled by local Border Patrol supervisors “far exceeds the number that are getting sent to the official investigators.”

Some of CBP’s reforms have clearly stalled, said Chris Rickerd, a senior policy counsel at the ACLU who tracks border issues, and Trump’s recurring rhetoric about getting tough at the border, Rickerd said, “sets precisely the wrong tone.”

Rickerd would like to see the agency get body cameras out into the field. While CBP has tested out cameras in two pilot programs, it still has not adopted the technology, which is common in many big city police departments. The cameras could help cut down on abusive behavior, Rickerd said.

In Kerlikowske’s view, Border Patrol agents would welcome body cameras. “The difficulty we had was finding a camera that could withstand the terrain,” he said of the harsh climate along the southern border. “The cameras we tested back then were pretty much gummed up by the dust or the dirt within about two months.” He also noted that at an agency the size of CBP, the costs of storing the vast amounts of footage accrued could be massive.

Bratton and his panel also encouraged CBP to revamp the penalties for employees who flout agency rules — and to create “mandatory consequences for the most serious offenses.” Today, the new penalty guidelines are still a work in progress. CBP said they are “currently under final review” but are not yet in effect.

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Perhaps the most important recommendation made by Bratton and the other members of the advisory panel regarded staffing. In the view of the panel, CBP needed to add some 350 internal affairs investigators to keep up with the number of complaints streaming into the agency. The panel said CBP should hire them over the next three years.

Since then, the agency has added about 50 new investigators and said it has received funds to hire 30 more.

“They staffing component continues to be a concern. I’m glad they’re working on it. But they’re not there,” Williams said. “And, of course, I think there’s a role for Congress to make it a funding priority.”

Some wonder whether the union representing Border Patrol agents, the National Border Patrol Council, is working to stifle changes that would impact its members. The union has achieved a new level of prominence in the Trump era, with union head Brandon Judd appearing frequently on Fox News to champion the president’s hardline approach to immigration policy; Trump has often spoken and tweeted his support for Judd, a tough-talking veteran who has spent more than two decades with the Border Patrol.

The union did not respond to questions about its stance on various reform proposals.

“I think there’s a lot of resistance from the union,” said Slack, who is the author of “Deported to Death: How Drug Violence is Changing Migration on the U.S.-Mexico Border.” “The union is a very powerful voice for a much more radical vision of what border enforcement can be. They have a vision of the Border Patrol as a paramilitary force.”