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WASHINGTON — Former FBI agent Michael German thought the agency had the information it needed to see the 9/11 terrorist attacks coming. In the aftermath of the attack, German reported a cover-up of a failed counterterrorism investigation that infringed upon people’s civil liberties in unprecedented ways.

Yet when German raised these concerns, the Department of Justice inspector general failed to investigate, he said. He also said the IG Office failed to protect him from official retaliation within the FBI, including possible surveillance, resulting in the 16-year veteran resigning in 2004.

“I tried to challenge the system from within, but they don’t like that,” German said in an interview with the American Civil Liberties Union. “They made it very uncomfortable so I finally realized it was time to work on the outside.”

German’s case became one of the most visible examples of the challenges facing whistleblowers in the intelligence community. In addition to a legal framework that makes it incredibly difficult for whistleblowers to come forward, a more subtle influence lurks beneath the surface: a culture that views whistleblowers as traitors, not reformers.

A new report by the Government Accountability Office released last Thursday found that, despite recent efforts to extend whistleblower protections to FBI employees, they remain exposed to retaliation for reporting wrongdoing.

Under the Whistleblower Protection Act of 1989, federal employees are generally protected from retaliation for reporting wrongdoing, entitling them to pursue legal recourse should they face retribution. However, FBI employees were excluded from these protections, and in 1998 the Department of Justice established separate guidelines that were meant to protect whistleblowers within the agency.

Yet the guidelines permitting FBI agents to disclose wrongdoing are unclear, according to the GAO report. For example, FBI employees must report wrongdoing only to a handful of designated officials. As a result, more than half of the 62 cases reviewed by the GAO were dismissed without review.

According Steven L. Katz, formerly counsel to the Senate Committee on Governmental Affairs and an expert on federal whistleblowing law, those in the FBI face much deeper issues than simply unclear legal guidelines. Instead, intelligence agents are a part of a culture that targets whistleblowers and punishes their behavior.

“When someone raises concerns, do you throw them overboard, or do you sit down with them and thank them?” he said. “The FBI throws them overboard.”

Katz argued that the GAO report fails to reflect the human aspect of the FBI in making it difficult for whistleblowers to come forward, focusing instead solely on the regulations that govern whistleblowing activities.

“The agencies are full of people, not just processes,” Katz said. “It’s the people who screw up because the laws look perfect on the books.”

According to Katz, other government agencies have faced similar problems with whistleblower culture. Last year, a series of attempted break-ins at the White House prompted Secret Service Director Julia Pierson to resign. A report released after the incident found that the Secret Service was “too insular,” ignoring the warning signs made plain by the attacks.

“In the agencies where you have a law enforcement culture, where power is might, people tend to transfer that culture of enforcement that’s outward facing inwards,” he said.

In 2012, President Barack Obama released Presidential Policy Directive 19, which established whistleblowing protection for those in the intelligence community. Elements of the directive were codified under the Intelligence Authorization Act for FY2014, but the guidelines of the directive aren’t permanent and can be easily reversed by a different president.

The result adds up to a climate that, while improving in some key ways, remains hostile to the act of whistleblowing. In an organization that possesses some of the nation’s most important classified information, the threat to the success of the FBI is intimately tied to the future of the country itself, as the 9/11 attacks demonstrated.

“You want the FBI to be effective, and so to help them be more effective you’d expect them to have better protection against retaliation from reporting problems,” said David Maurer, director for GAO’s homeland security and justice department. “It’s ironic that they have less whistleblower protection than the rest of the government.”