Brookings Institution's Gen. John Allen resigns amid foreign lobbying investigation

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The Brookings Institution's president, retired four-star Gen. John R. Allen announced that he is resigning from the organization amid a federal investigation into his alleged role doing illegal foreign lobbying work for Qatar. Allen was placed on administrative leave on May 10.

Allen said in a resignation letter that his decision is "best for all concerned in this moment," according to the Wall Street Journal.

"While I leave the institution with a heavy heart, I know it is best for all concerned in this moment," Allen said in the resignation letter.

The Brookings Institution thanked Allen for his leadership during the pandemic, according to the report.

The decision comes after new federal court filings spell out a potential criminal case against Allen, who joined Brookings in 2017 after leading NATO and U.S. forces in Afghanistan.

Court filings allege that Allen worked to help Qatar influence U.S. policy during a period of time when there was a diplomatic crisis in the Gulf region.

In a search warrant application, Federal Bureau of Investigations Agent Babak Adib wrote that there is "substantial evidence" that Allan violated the Foreign Agents Registration Act (FARA). Allan has not been charged with any crime. 

RETIRED GEN. ALLEN PUSHES BACK ON ALLEGATIONS THAT HE LOBBIED FOR QATAR DURING 2017 GULF BLOCKADE

FILE - Marine Gen. John Allen, the top U.S. commander in Afghanistan, testifies on Capitol Hill in Washington on March 20, 2012. A former high-ranking U.S. ambassador admitted Friday, June 3, 2022, to illegal foreign lobbying on behalf of Qatar after demanding that prosecutors tell him why Allen, a retired four-star general who worked with him on the effort, has not been charged.  (AP Photo/J. Scott Applewhite, File)

In a June 10 announcement from the Brookings Institution, the organization announced that Ted Gayer has been appointed acting president. Gayer has been Brookings's executive vice president since 2018, according to the announcement.

The statement also says that the "integrity and objectivity of Brookings scholars and their research constitute the institution’s principal assets."

"Brookings seeks to maintain high ethical standards in all its operations. Brookings has strong independence policies in place to ensure financial supporters do not influence the research findings or policy recommendations of its experts," the statement reads. 

"Brookings is not the subject of a federal investigation into a personal trip Allen took to Qatar in 2017 before he became president of the institution. Brookings receives no funds from the government of Qatar. Brookings received funding from Qatar in the past to support operations for research and events. In early 2019, Brookings decided it would not renew funding from the country and would close its Brookings Doha Center, established in 2007. The decision to close the Brookings Doha Center was concurrent with the decision to transition all of Brookings’s foreign centers," it continued.

City Skyline and buildings  - Doha , Qatar

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The case against Allen is in relation to a 2017 crisis when several nations announced a blockade against Qatar because of a dispute that was related to a number of issues. Former President Trump appeared to side with Qatar during the incident, but the court filings allege that Allen lobbied then-National Security Advisor H.R. McMaster and played an important role in shifting the response by the United States.

The FBI says that Allen gave a "false version of events" when talking with law enforcement in 2020 about his work for Qatar, adding that he failed to produce relevant email messages when earlier subpoenaed by a grand jury.

File photo of former National Security Advisor H.R. McMaster. (Photo by Jabin Botsford/The Washington Post via Getty Images)

Allen's spokesman, Beau Phillips, said in a statement that the retired four-star has done nothing that's against the law.

"Through decades of public service in combat and diplomacy, General Allen has earned an unmatched, sterling reputation for honor and integrity," Phillips said. "We look forward to correcting the falsehoods about General Allen that have been improperly publicized in this matter." 

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Phillips told Fox News Digital that Allen's counsel is "deeply concerned" with the public release of the search warrant.

"General Allen’s counsel is deeply concerned about the serious and damaging ethical breach that occurred with the public release of a search warrant affidavit containing confidential grand jury information," Phillips said. "Not only did the breach offend longstanding law and Department of Justice policy on the confidentiality of ongoing investigations, but the narrative presented in the affidavit and now made public also is factually inaccurate, incomplete, and misleading."

The Foreign Agents Registration Act requires anyone engaged in domestic work of political nature on behalf of another country or a foreign interest to register with the Department of Justice and disclose any information that is related to financial compensation.

Fox News' Peter Aitken and Andrew Murray contributed to this report.