U.S. Border Patrol agents detain a smuggling suspect July 24 in Mission, Texas. The former head of internal affairs at U.S. Customs and Border Protection has alleged that the agency is dogged by corruption and coverups. (John Moore/Getty Images)

At least a quarter of the 28 fatalities at the hands of U.S. Customs and Border Protection agents and officers since 2010 were “highly suspect” and officials have distorted facts to try to hide any missteps, alleges James F. Tomsheck, CBP’s former head of internal affairs.

The agency removed Tomsheck in June, calling for more aggressive probes into excessive use of force and abuse. But Tomsheck, who still works for CBP, said his efforts were hindered by officials at an agency rife with coverups and corruption.

His first public comments about the agency’s problems since his removal were made in an exclusive and unauthorized interview with the Center for Investigative Reporting.

Tomsheck has also given closed-door briefings to Senate Homeland Security and Governmental Affairs and House Oversight and Government Reform committee leaders. And the Office of Special Counsel is considering a whistleblower retaliation claim Tomsheck recently filed.

The embattled agency has faced mounting criticism for border shootings, a crisis underscored by a scathing 2013 independent report of 67 cases. But even that report doesn’t fully capture CBP’s culture of distorting facts to guarantee that a questionable shooting looks like “a good shoot,” Tomsheck said.

“In nearly every instance, there was an effort by Border Patrol leadership to make a case to justify the shooting versus doing a genuine, appropriate review of the information and the facts,” he said.

He declined to cite specific examples because many cases still may be under review.

Tomsheck, who held his post for eight years, has been assigned to the Border Patrol as its executive director for national programs.

R. Gil Kerlikowske, the CBP commissioner, has pledged reforms and called for a review of the shootings enumerated in the 2013 report. CBP also tightened restrictions on the use of lethal force this spring, but the agency declined to comment on Tomsheck’s allegations.

In addition to shooting coverups, he alleges:

●The agency’s corruption includes taking bribes from those smuggling drugs or people into the country and stealing government property. An estimated 5 to 10 percent of border agents and officers are corrupt or were at some point in their career, Tomsheck said.

“To a large degree, it [corruption] was an undetected problem and far more severe than the actual number of arrests” of corrupt employees, he said.

Tomsheck believes thousands of employees hired during an unprecedented expansion in the post-9/11 era may be unfit to carry a badge and gun. He is certain criminals have entered its law-enforcement ranks, which now number more than 43,000. Others may pose security risks because of past criminality, links to criminal organizations and drug use.

Polygraph exams for applicants tell the story, Tomsheck said. Approximately 55 percent of applicants get disqualified by the polygraph, which wasn’t mandatory for all job seekers until 2013. Since October 2004, roughly 170 CBP employees, including Border Patrol agents, have been arrested or convicted on corruption-related charges.

●The agency’s problems are rooted in border politics, internal policy and the Border Patrol’s warped view of itself — what Tomsheck called “institutional narcissism” — the belief that it is the premier federal law-enforcement agency. That idea, he added, is part of a broader culture of impunity within the Border Patrol, which believes it is beyond “constitutional constraints” and rejects outside scrutiny.

“It has been suggested by Border Patrol leadership that they are the Marine Corps of the U.S. law-enforcement community,” he said. “The Border Patrol has a self-identity of a paramilitary border security force and not that of a law-enforcement organization.”

●Such attitudes, Tomsheck said, played into hampering his efforts to investigate shootings.

Senior officials at Customs and Border Protection and elsewhere in the Department of Homeland Security interfered with, blocked or delayed his efforts against corruption, abuse and other misconduct — including civil rights violations — by telling his office to back off or stand down, he said.

Tomsheck said he was criticized and ultimately retaliated against for not following the agency’s “corporate message” on corruption by “redefining” it so it appeared to be less of an issue.

His sharpest battles came during the first Obama administration, when Alan Bersin, a former U.S. attorney in San Diego, was the commissioner and David Aguilar was his deputy. Aguilar eventually became the acting commissioner.

Aguilar played down corruption, according to an earlier whistleblower complaint Tomsheck filed with the Office of Special Counsel.

According to the 2011 complaint, in a private meeting in March 2010, Aguilar scolded Tomsheck for being candid about the agency’s integrity issues at a Senate hearing a week earlier. Aguilar yelled at Tomsheck, the complaint alleges, describing his testimony as “not part of his ‘corporate message’ on corruption.”

In another closed-door meeting on April 15, 2010, Aguilar tried to pressure Tomsheck and his then-deputy, James Wong, into redefining corruption to include only “mission-critical” compromises, such as taking bribes or other payment to aid drug traffickers and human smugglers. When Tomsheck balked, Aguilar retaliated by penalizing his performance review, Tomsheck alleged. The negative review was later reversed by CBP.

In addition to CBP, the Homeland Security Department inspector general’s office and Aguilar declined to comment. Bersin did not respond to a request for comment.

Bersin, who left Customs and Border Protection at the end of 2011, is the assistant secretary for international affairs at Homeland Security and its top diplomatic officer. Aguilar retired in March 2013.

In an interview last month, Kerlikowske did not respond directly to questions about how internal affairs had not been aggressive but said he was looking for a different or fresh perspective when he reassigned Tomsheck. He has tapped an FBI agent to helm the internal affairs office in the interim.

“I have nothing but the highest regard for Jim — and told him so — and believe he can be very worthwhile,” Kerlikowske said.

Other officials have supported Tomsheck’s accusations.

In briefings to the FBI in fall 2012, senior CBP leaders outside internal affairs pegged the corruption rate at one time or another at 20 percent or more.

Shocked at that “integrity gap,” the FBI adjusted its priorities to focus its anti-corruption efforts on federal employees, with an emphasis on border agents and officers, said Ronald Hosko, a retired FBI assistant director for the criminal investigative division who attended the briefings.

“The FBI remains committed to working with all of its interagency partners to address corruption and is actively engaged in working to ensure the cooperation between the FBI and its partners remains strong,” said Joseph S. Campbell, the current assistant director for the criminal investigative division.

“As Jim’s concerns grew into suspicion, other CBP officials began to look at him and say, ‘He’s distrustful of us all,’ ” Hosko said. “But when 10 to 20 percent of the workforce is suspected of corruption is thrown on the table, that’s chilling. Cut that number in half, and it’s still chilling.

“As his distrust grew, he was painted as paranoid. But they gave him plenty of reasons to be distrustful.”

In recent years the annual number of busts of corrupted employees has slowed, but Tomsheck and Hosko attribute it to a failure to share information properly among anti-corruption agencies, including the inspector general’s office and the FBI.

A spokesman for the National Border Patrol Council, the union that represents 17,000 Border Patrol agents and support staff, disputed allegations about excessive use of force. Shawn Moran said agents use force reluctantly and only when necessary.

Thorough outside investigations have yet to show that an agent’s use of deadly force was unjustified, he said. He criticized Tomsheck for not raising his concerns — including with the union — when he headed internal affairs.

Agents in the field don’t see themselves as a paramilitary force, he said. Nor do they want to work with corrupt agents or people unsuitable for law enforcement slots.

“They want to do their jobs. They want to be compensated fairly. And they want to go home safe at the end of the night,” he said. “We had anti-terrorism shoved down our throat.”

Not all of the more than half-dozen fatal cross-border shootings are questionable, Tomsheck said. In one recent review of a lethal shooting he signed off on before his ouster, he found an agent had acted accordingly to protect a fellow agent.

Yet Border Patrol leadership had falsely reported on at least one occasion that a person had been on U.S. soil when agents fatally shot him, but that “was clearly not the case,” Tomsheck said.

Becker covers border, immigration and national security issues for the Center for Investigative Reporting, an independent, nonprofit newsroom based in the San Francisco Bay Area. For more, visit www.cironline.org. Becker can be reached at abecker@cironline.org. Follow him on Twitter: @abeckerCIR.