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The Defense Intelligence Agency has suspended the security clearance it granted to former national security adviser Michael Flynn in the latest blow to the embattled retired general.

DIA spokesman James Kudla said the suspension took effect Tuesday night. That was one day after Flynn resigned after it was revealed that he had misled White House officials about his contacts with the Russian ambassador to the United States.

"We thought it was prudent to take a pause on his access to classified information," Kudla said, given "all the questions" around Flynn's conduct. He declined to be more specific.

Officially, Kudla said, the DIA was examining Flynn's "compliance with intelligence community security clearance directives."

Flynn did not immediately respond to NBC News' request for comment.

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Flynn was forced to resign after it became public that he misled White House officials when he told them he did not speak to the Russian ambassador about the U.S. sanctions on Russia. FBI transcripts show that the subject was discussed, officials say.

Related: A Timeline of Mike Flynn's Rise and Fall and the Russia Call

"The evolving, and eroding level of trust as a result of this situation in a series of other questionable instances is what led the president to ask for General Flynn's resignation," White House press secretary Sean Spicer said told reporters on Tuesday.

Spicer did not further discuss what the "other questionable instances" were.

Yet after his spokesman said Tuesday that Flynn lost the president's confidence, Trump appeared to cast the matter Wednesday as a problem with news media leaks.

"From intelligence, papers are being leaked, things are being leaked," Trump said at a White House news conference with Israeli Benjamin Netanyahu. "It's a criminal action, criminal act, and it's been going on for a long time before me, but now it's really going on. And people are trying to cover up for a terrible loss that the Democrats had under Hillary Clinton."

Related: Trump Blames Russian Connection 'Conspiracy Theories' on Clinton Campaign 'Cover Up'

Earlier, on Twitter, Trump said that "The real scandal here is that classified information is illegally given out by 'intelligence' like candy. Very un-American!"

Kudla said the suspension was an administrative procedure that did not reflect any adverse finding against Flynn.

Mark Zaid, a Washington attorney who represents intelligence officials in clearance disputes, said that in his experience the sort of suspension Flynn has received can be indefinite, particularly since Flynn does nor currently hold a job that requires access to classified material.

"This is a preliminary preemptive action they take when something has come to their attention that requires further examination," Zaid said.

Flynn, a retired Army lieutenant general, ran the Defense Intelligence Agency from 2014 to 2014. The DIA typically grants clearance to its former directors so that current directors can consult them. Kudla said.

Flynn was in the process of having his clearance transferred to a higher status as national security adviser when he resigned, Kudla said. That left the DIA as the sole agency granting Flynn access to secrets.