WASHINGTON — John R. Allen, the retired four-star general who once commanded American troops in Afghanistan, has been placed on administrative leave as president of the Brookings Institution amid a federal inquiry into whether he secretly lobbied for the government of Qatar, the think tank announced on Wednesday.

The decision was released in an email by the leaders of the board of trustees of the prestigious, left-leaning institution. It came a day after The New York Times and The Associated Press revealed that federal prosecutors had obtained records indicating that General Allen engaged in the lobbying effort, lied to investigators about his role and tried to withhold evidence sought by a federal subpoena.

“We want to assure you that Brookings is not a subject of this investigation,” the announcement said. “Brookings has strong policies in place to prohibit donors from directing research activities.”

Prosecutors outlined the secret lobbying plan in an April application for a warrant to search General Allen’s electronic communications. In the document, prosecutors cited messages from General Allen about his plans to make money off a 2017 initiative to defuse the diplomatic crisis between Qatar and its rivals in the Middle East, Saudi Arabia and the United Arab Emirates.

During the height of the crisis in June 2017, General Allen traveled to Doha, the Qatari capital, with Richard G. Olson, a former U.S. ambassador, and Imaad Zuberi, a business executive with ties to the Middle East. The court document states that General Allen made the trip at Mr. Zuberi’s expense and negotiated a payment of $20,000, which he referred to as a “speaker’s fee.”

The document quotes one message from General Allen showing he hoped to make more money in the future, to “work out a fuller arrangement of a longer term relationship,” as he put it.

After the trip, during which General Allen met with top Qatari officials, he returned to Washington and lobbied members of Congress and the Trump administration on behalf of Qatar, according to the document.

The trip occurred after General Allen had retired from government service and moved to the Brookings Institution but before he became president of the think tank.

Mr. Zuberi is serving a prison sentence for violating foreign lobbying, campaign finance and tax laws, as well as for obstruction of justice.

Beau Phillips, a spokesman for General Allen, called the narrative presented in the document “factually inaccurate, incomplete and misleading.”

“General Allen has done nothing improper or unlawful, has never acted as an agent of Qatar or any foreign government or principal and has never obstructed justice,” Mr. Phillips said in a statement on Wednesday. “Through decades of public service in combat and diplomacy, General Allen has earned an unmatched, sterling reputation for honor and integrity.”

Brookings once maintained a large campus in Doha, and the government of Qatar was a significant source of Brookings’s funding. On Wednesday, a Brookings spokeswoman wrote in a message that in 2019, during General Allen’s tenure as president, the think tank decided to end its affiliation with the Doha center and the other campuses it maintained in foreign countries.

“This separation is now complete, and the new center, which has no affiliation with Brookings, is named the Middle East Council on Global Affairs,” said the spokeswoman, Andrea Risotto.

“Brookings currently receives no funds from Qatar.”