Lt. Gen. Michael Flynn arrives for a meeting with US President-elect Donald Trump at Trump Tower December 12, 2016 in New York.
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FILE - In this Feb. 1, 2017 file photo, National Security Adviser Michael Flynn speaks during the daily news briefing at the White House, in Washington. A lawyer for former national security adviser Flynn has told President Donald Trump's legal team that they are no longer communicating with them about special counsel Robert Mueller's investigation into Russian election interference, according to a person familiar with the decision who spoke to The Associated Press on condition of anonymity. (AP Photo/Carolyn Kaster, File)
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FILE - In this Feb. 1, 2017 file photo, National Security Adviser Michael Flynn speaks during the daily news briefing at the White House, in Washington. A lawyer for former national security adviser Flynn has told President Donald Trump's legal team that they are no longer communicating with them about special counsel Robert Mueller's investigation into Russian election interference, according to a person familiar with the decision who spoke to The Associated Press on condition of anonymity. (AP Photo/Carolyn Kaster, File)
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WASHINGTON, DC - JANUARY 20: Retired Army Lt. General Michael Flynn arrives for the Presidential Inauguration of Donald Trump at the US Capitol on January 20, 2017 in Washington, DC. Flynn is appointed National Security Advisor to Trump. Donald J. Trump will become the 45th president of the United States today.  (Photo by Saul Loeb - Pool/Getty Images)
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WASHINGTON, DC - JANUARY 20: Retired Army Lt. General Michael Flynn arrives for the Presidential Inauguration of Donald Trump at the US Capitol on January 20, 2017 in Washington, DC. Flynn is appointed National Security Advisor to Trump. Donald J. Trump will become the 45th president of the United States today. (Photo by Saul Loeb - Pool/Getty Images)
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NEW YORK, NY - NOVEMBER 17: Retired Lt. Gen. Michael Flynn gestures as he arrives at Trump Tower, November 17, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
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NEW YORK, NY - NOVEMBER 17: Retired Lt. Gen. Michael Flynn gestures as he arrives at Trump Tower, November 17, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
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Former Trump national security adviser Michael Flynn, center, arrives at federal court in Washington, Friday, Dec. 1, 2017. Court documents show Flynn, an early and vocal supporter on the campaign trail of President Donald Trump whose business dealings and foreign interactions made him a central focus of Mueller's investigation, will admit to lying about his conversations with Russia's ambassador to the United States during the transition period before Trump's inauguration.  (AP Photo/Susan Walsh)
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Former Trump national security adviser Michael Flynn, center, arrives at federal court in Washington, Friday, Dec. 1, 2017. Court documents show Flynn, an early and vocal supporter on the campaign trail of President Donald Trump whose business dealings and foreign interactions made him a central focus of Mueller's investigation, will admit to lying about his conversations with Russia's ambassador to the United States during the transition period before Trump's inauguration. (AP Photo/Susan Walsh)
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NEW YORK, NY - DECEMBER 12: Retired Lt. Gen. Michael Flynn, President-elect Donald Trump's choice for National Security Advisor, waits for an elevator in the lobby at Trump Tower, December 12, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
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NEW YORK, NY - DECEMBER 12: Retired Lt. Gen. Michael Flynn, President-elect Donald Trump's choice for National Security Advisor, waits for an elevator in the lobby at Trump Tower, December 12, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
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NEW YORK, NY - NOVEMBER 29:  General Mike Flynn, Donald Trump's new national security adviser, arrives at Trump Tower on November 29, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration.  (Photo by Spencer Platt/Getty Images)
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NEW YORK, NY - NOVEMBER 29: General Mike Flynn, Donald Trump's new national security adviser, arrives at Trump Tower on November 29, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration. (Photo by Spencer Platt/Getty Images)
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Story highlights

Flynn has been at the center of a controversy over his contacts with the Russian ambassador to the US

He may have misled the Vice President about those calls

(CNN) —  

The Justice Department warned the Trump administration last month that Michael Flynn misled administration officials regarding his communications with the Russian ambassador to the United States and was potentially vulnerable to blackmail by the Russians, a person familiar with the matter told CNN.

Flynn resigned his position as national security adviser shortly after the reports emerged Monday night.

A White House official also confirmed the warning.

Flynn resigns amid controversy over Russia contacts

The concern was raised after Flynn claimed he did not discuss with the Russian ambassador the sanctions being imposed by former President Barack Obama’s administration in retaliation for Russia’s interference in the election. Flynn was not yet in government.

The message was delivered by then-Acting Attorney General Sally Yates. Other top intelligence officials, including James Clapper and John Brennan, were in agreement the White House should be alerted about the concerns.

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Spicer: Trump is evaluating Flynn situation

The Washington Post first reported the Justice Department message.

Trump fired Yates at the end of January after she told Justice Department attorneys not to defend his executive order suspending the refugee program and temporarily restricting travel to the US from seven majority-Muslim nations. Implementation of the travel ban has since been stalled by the courts and the Trump administration is weighing its options.

A representative for Yates said she no comment.

Flynn situation is ‘fluid,’ source says

Flynn is a retired lieutenant general who was the head of the Defense Intelligence Agency under Obama until he was forced out. His resignation less than a month into the Trump presidency marked the second consecutive administration under which Flynn had risen and fallen.

He had been at the center of mounting controversy over the past several days in regard to his contacts with Russian Ambassador Sergey Kislyak. Following initial reports in early January that Flynn was in contact with Kislyak and spoke to him about US sanctions, Vice President Mike Pence offered a robust defense of the incoming national security adviser. He said in nationally televised interviews that he had spoken with Flynn and that Flynn had ensured him he had not spoken about sanctions with the Russian ambassador.

But reports of an investigation showed Flynn potentially misled Pence and criticism of the controversial former military man grew.

Flynn wrote in his resignation letter that he had “inadvertently” briefed Pence and others in the White House with incomplete information about his contacts with Kislyak.

The resignation capped off a a day during which Flynn’s public standing within the White House had quickly shifted.

White House senior counselor Kellyanne Conway said on Monday the President had “full confidence” in Flynn. But about an hour later, things had changed.

White House press secretary Sean Spicer offered a much more limited commitment from the President towards Flynn, saying Trump was “evaluating the situation.”

An administration official said new information came to light between Conway’s comments and the Spicer statement.

Another source said Conway “did not go out there on her own” to say the President had full confidence in Flynn, and that “new information came to light in real time.”

CNN’s Jim Acosta, Dana Bash and Gloria Borger contributed to this report.