The FBI has confirmed to a senior Republican senator that agents were sworn to secrecy -- and subject to lie detector tests -- in the Hillary Clinton email probe, an extensive measure one former agent said could have a "chilling effect."

A July 1 letter sent by a senior deputy to FBI Director James Comey to Senate Judiciary Committee Chairman Charles Grassley, R-Iowa, detailed the restrictions on agents. The letter, reviewed by Fox News, confirmed agents signed a "Case Briefing Acknowledgement" which says the disclosure of information is "strictly prohibited" without prior approval, and those who sign are subject to lie detector tests.

"The purpose of this form is to maintain an official record of persons knowledgeable of a highly sensitive Federal Bureau of Investigation counterintelligence investigation," the agreement attached to the Grassley letter reads, "....I (FBI agent) also understand that, due to the nature and sensitivity of this investigation, compliance with these restrictions may be subject to verification by polygraph examination."

The measures show the extent to which the bureau has gone to keep additional details of the politically sensitive case from going public. While Comey has provided some information ‎on why the FBI did not opt to pursue charges, Attorney General Loretta Lynch repeatedly ducked questions on specifics of the case at a House hearing Tuesday.

A recently retired FBI agent, who declined to speak on the record, citing the sensitivity of the matter, said a "Case Briefing Acknowledgement" is reserved for "the most sensitive of sensitive cases," and can have a "chilling effect" on agents, who understand "it comes from the very top and that there has to be a tight lid on the case."

The former agent said the agreements can also contribute to "group think" because investigators cannot bounce ideas off other agents, only those within a small circle.

Grassley first wrote to the FBI Director February 4 after a Fox News report that agents were asked to sign additional non-disclosure agreements. In his response to the senator, the FBI's Assistant Director, Office of Congressional Affairs, Stephen D. Kelly, said “this was not a unique circumstance” and agents "may from time to time be asked to sign similar forms.”

The July letter also says that the purpose of the agreement was two-fold: "to maintain an official record of all persons knowledgeable of this highly unusual investigation, and to remind individuals of their obligations to protect classified and sensitive information."  The letter states "no one refused to sign" or “raised any questions or concerns.”

Comey said last week more than 100 classified emails were sent or received by Hillary Clinton, including some at the Top Secret level, which would require agents to have the necessary clearance to review and investigate.  Some of the intelligence came from the U.S. government's most closely held programs, known as Special Access Programs, or SAP and included human spying.

The "Case Briefing Acknowledgement" is more evidence that the probe was always a serious criminal investigation, and never a "security review" or "security inquiry" as described by Clinton and her campaign team.

Responding one day after the FBI director said he would not recommend criminal charges, Grassley pointed to Comey's conclusions that a limited number of emails had classified markings, thousands of work related emails were not turned over by Clinton to the State Department despite a sworn declaration to a federal court and her public assurances, as well as "potential violations of the statutes regarding the handling of classified information."

"In light of all these inconsistencies, it is even more troubling that the FBI tried to gag its agents with a non-disclosure agreement on this matter, in violation of whistleblower protection statutes,"  Grassley said in the strongly worded letter.  "...you indicated that agents working on this case were required to sign a non-disclosure agreement that failed to exempt protected whistleblowing. Only after I wrote to you did you advise your FBI agents that they are still free to speak with Congress regarding waste, fraud, and abuse."

The "Case Briefing Acknowledgement Addendum" provided to Senator Grassley after the initial FBI response July 1 makes clear the agreement does not supersede or conflict with "communications to Congress" and "the reporting to an Inspector General of a violation, or a substantial and specific danger to public health or safety, or….any other whistleblower protection."

Grassley also noted the timing of the FBI's response five months after his original request for information on the NDAs, with a partial response July 1, and full response on July 5 2016, the same day the FBI made a public recommendation at bureau headquarters against criminal charges.

The New York Post first reported that the "Case Briefing Acknowledgement" was signed by the Clinton email agents, citing anonymous sources, but the Grassley letter is believed to be the first public acknowledgement by the FBI, and includes a sample copy of the non-disclosure agreement.

Grassley’s letter is wide ranging, and beyond the non-disclosure agreements, requests a response by July 20 to questions including whether, after Bill Clinton and Lynch’s June 28 meeting on a Phoenix airport tarmac, there is no need for a special counsel. He also wanted to know about  the FBI’s reported agreement that some questions would be off limits for Clinton’s personal attorney Cheryl Mills, and whether the FBI or Justice Department raised concerns that several of Clinton’s associates used the same attorneys to represent them in the investigation.