For sixteen years, Michael German worked for the FBI as a special agent in domestic terrorism, bank fraud and public corruption investigations. In 2004 he resigned and went public about continuing deficiencies in FBI counterterrorism operations after the implementation of 9/11 Commission reforms. He's now a Fellow at the Brennan Center For Justice at NYU's school of law. (Linda Davidson/The Washington Post)

In early April, Sen. Charles E. Grassley summoned FBI officials to his Capitol Hill office. He said he wanted them to explain how a program designed to uncover internal security threats would at the same time protect whistleblowers who wanted to report wrongdoing within the bureau.

The meeting with two FBI officials, including the chief of the bureau’s Insider Threat Program, ended almost as soon as it began. The officials said the FBI would protect whistleblowers by “registering” them. When Grassley’s staff members asked them to elaborate, the FBI officials declined to answer any more questions and headed for the door.

“We’re leaving,” said J. Christopher McDonough, an FBI agent assigned to the bureau’s congressional affairs office, said Senate staff members who attended the meeting.

The episode infuriated Grassley (Iowa), a leading advocate for whistleblowers in Congress and the ranking Republican on the Senate Judiciary Committee. Any effort to register whistleblowers, he said, would “clearly put a target on their backs.”

The Insider Threat Program and a continuous monitoring initiative under consideration in the intelligence community were begun by the Obama administration after the leaks of classified information by former NSA contractor Edward Snowden and Army Pvt. Chelsea Manning, and the Navy Yard shootings by Aaron Alexis, who used his security clearance to gain access to the base.

The programs are designed to prevent leaks of classified information by monitoring government computers and employees’ behavior.

Grassley said the episode with the FBI illustrates how federal agencies are setting up internal security programs without giving careful consideration to whether they could dissuade whistleblowers from coming forward.

“The Insider Threat Program has the potential for taking the legs out from underneath all of the whistleblower protections we have,” Grassley said in a recent interview.

Greg Klein, the head of the FBI’s Insider Threat Program, and McDonough, the congressional affairs agent, did not return calls seeking comment. An FBI spokesman said the bureau does not plan to register whistleblowers. He said there was a misunderstanding about the nature of the briefing with staff members for Grassley, Judiciary Committee Chairman Patrick J. Leahy (D-Vt.) and a law enforcement official who is assigned to the Senate panel. The spokesman noted that the FBI has a whistleblower training program for employees and a whistleblower protection office.

“We recognize the importance of protecting the rights of whistleblowers,” FBI spokesman Paul Bresson said.

Grassley is part of a growing chorus of lawmakers on Capitol Hill and attorneys for whistleblowers who warn that the Insider Threat Program and the potential intelligence community initiative threaten to undermine federal workers’ ability to report wrongdoing without retaliation.

Together, the programs cover millions of federal workers and contractors at every government agency.

In February, Director of National Intelligence James R. Clapper Jr. testified before the Senate Armed Services Committee that a system was being considered to continuously monitor the behavior of employees with security clearances “on the job as well as off the job.”

A senior intelligence official said a continuous monitoring program, mandated under the Intelligence Authorization Act and signed into law by President Obama on July 7, is being set up and initially will include federal employees who hold top-secret security clearances. The official said there are no plans to monitor employees after hours while they are using non-government computer systems.

“I think it’s time to put up the caution light here,” said Sen. Ron Wyden (D-Ore.), a member of the Senate Intelligence Committee.

While Wyden included a provision in the most recent Intelligence Authorization Act that would prohibit retaliation against whistleblowers, he said he remains concerned about the impact of the threat programs.

“This really has the potential for abuse, and I think it could have a chilling effect on the public’s right to know and effective oversight of our government,” Wyden said.

Dan Meyer, the head of the Intelligence Community Whistleblowing & Source Protection program, created last year as part of the Office of Intelligence Community Inspector General, said he is working to ensure that employees who want to report wrongdoing can do so anonymously and without reprisal.

“The critical thing is to maintain confidentiality,” Meyer said. He said he is preparing training materials for intelligence officers and spreading the word that employees can come to him anonymously through third parties.

If an employee has verifiable information about wrongdoing, a presidential directive takes effect, providing employees with protection against retaliation.

“We are in the process of making a systematic, cultural change and getting everyone on board,” Meyer said.

After Manning’s disclosures to WikiLeaks four years ago, Obama signed Executive Order 13587, directing government agencies to assess how they handle classified information. On Nov. 28, 2010, the Office of the National Counterintelligence Executive issued a memo to senior government agency officials, advising them to identify insider threats.

The memo suggested using psychiatrists and sociologists to assess changes in employees’ behavior.

“What metrics do you use to measure ‘trustworthiness’ without alienating employees?” the counterintelligence office asked the agency chiefs. “Do you use a psychiatrist or sociologist to measure: relative happiness as a means to gauge trustworthiness? Despondence and grumpiness as a means to gauge waning trustworthiness?”

“It will only increase hostility between the government and really serious federal employees who are trying to improve the system,” said Lynne Bernabei, a partner at Bernabei & Wachtel in Washington who has been representing whistleblowers for nearly 30 years. “Turning the security apparatus against its own people is not going to work.”

Whistleblower lawyers said they understand the need to protect classified information but think some of the new programs go too far.

“There are legitimate reasons for employers to be on the lookout for people who might be leaking classified information, but this will obviously have a chilling effect on employees who might want to blow the whistle,” said Jason Zuckerman, who served as the senior legal adviser to the U.S. Office of Special Counsel, the federal agency charged with protecting whistleblowers, and now represents whistleblowers nationwide.

Michael German, a former undercover FBI agent and whistleblower, called the Insider Threat Program a “dangerous” initiative.

“These agencies have long treated whistleblowers as security threats and this makes things even worse,” said German, now a senior national security fellow at the Brennan Center for Justice at New York University School of Law.

Mark S. Zaid, a lawyer who specializes in representing whistleblowers in the intelligence community and the military, said the administration is moving too quickly.

“They are using a very big net to catch a few small fish, and they are going to hurt a lot of good people in the process,” he said.