Trump administration officials said on Thursday that Chris Krebs, who debunked President Trump’s lies about the 2020 election as head of the federal cybersecurity agency, lost his membership in an expedited customs program for travelers because he is facing a federal investigation.
The officials declined to specify why Mr. Krebs was under investigation, nor did they indicate which agencies were conducting the inquiry. The disclosure came three weeks after Mr. Trump, in an act of score settling and intimidation, directed the Justice Department to investigate Mr. Krebs.
“Chris Krebs is under active investigation by law enforcement agencies,” a spokesman for the Department of Homeland Security said in a statement. “That is a fact disqualifying him for global entry.”
The department offered no further explanation about the inquiry into Mr. Krebs, who was appointed to lead the Cybersecurity and Infrastructure Security Agency by Mr. Trump in 2018. Asked about the suspension of Mr. Krebs’s Global Entry travel program status, a White House official supplied a similar statement, offering no other details. The official did not respond to a follow-up question.
It is unusual for a government law enforcement agency to confirm or deny an open investigation. Mr. Trump has cited comparable breaches of protocol in accusing law enforcement of trying to smear him during various investigations into his conduct.
The Global Entry program, administered by U.S. Customs and Border Protection, a division of the Homeland Security Department, allows low-risk travelers who have passed a clearance process to avoid time-consuming screening procedures at airports.
Mr. Krebs was fired after the 2020 election when he pushed back on unsubstantiated claims by Trump allies that government super computers had secretly switched votes from Mr. Trump to Mr. Biden. He later created a website to fact-check allegations by Trump allies.
“The Nov. 3 election was the most secure in American history,” wrote Mr. Krebs, along with state election officials, in a statement posted to the cybersecurity agency’s website shortly before he was fired.
“There is no evidence that any voting system deleted or lost votes, changed votes, or was in any way compromised.”
The targeting of Mr. Krebs is the latest in a barrage of administration actions intended to punish, embarrass, threaten and inconvenience Mr. Trump’s perceived adversaries — in the case of Mr. Krebs, a respected public servant who offered a factual corrective to his fabrications.
Mr. Krebs received an email on Wednesday alerting him that his status in the Global Entry program had changed, prompting him to log into his account.
Even if Mr. Krebs is never charged, much less convicted, of any crime, the allegations require him to devote time and resources to defending himself. A week after Mr. Trump’s directive, Mr. Krebs resigned from the cybersecurity firm he had joined, to focus on fighting the investigation.
A Justice Department spokesman did not respond to a request for comment. Mr. Krebs had no comment.
In a memo Mr. Trump signed on April 9, he accused Mr. Krebs, a widely respected cybersecurity executive, of being “a significant bad-faith actor who weaponized and abused” his authority as a government official.
Among his purported misdeeds listed on the memo were “the censorship of disfavored speech implicating the 2020 election and Covid-19 pandemic” and the suppression of “conservative viewpoints under the guise of combating supposed disinformation.”
Mr. Krebs was also stripped of his security clearance.
Since taking the presidency for a second time, Mr. Trump has been systematically working through targets for retribution, most notably law firms that he has issued or threatened to issue executive orders against.
The directive related to Mr. Krebs was the first time since taking office again that Mr. Trump had publicly ordered investigations into individuals. Miles Taylor, a Homeland Security Department official in the first Trump administration who has been deeply critical of Mr. Trump, was also singled out.
Eileen Sullivan is a Times reporter covering the changes to the federal work force under the Trump administration.
Glenn Thrush covers the Department of Justice for The Times and has also written about gun violence, civil rights and conditions in the country’s jails and prisons.
Maggie Haberman is a White House correspondent for The Times, reporting on President Trump.
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