Flynn pleaded guilty of lying to the Federal Bureau of Investigation on Friday.
A message McFarland sent on December 29 while serving on the Trump transition team appears to be in conflict with her remarks before Congress, according to an email obtained by the Times.
And CBS is reporting she also spoke to Flynn about it.
"There's no question that this is going to create a major pause in her nomination".
McFarland's confirmation is in doubt over her role during the Trump transition and as the deputy to Flynn at the National Security Council.More news: FY2017 EPS Estimates for Golar LNG Partners LP Reduced by Analyst (GMLP)
Though the U.S. foreign relations committee approved the nomination in September despite the opposition of nearly every Democratic member, but no vote on McFarland has been scheduled in the full Senate.
In a statement Monday, Mr Booker said that he was concerned that Ms McFarland might have answered falsely.
Here's what we learned last week when Mueller's team unveiled its plea deal with Trump's former national security adviser, retired Gen. Michael Flynn.
So let's see, which Trump associates or officials have so far been caught lying about meetings with the Russians?
Flynn talked to Mr Kislyak by phone on Dec 29, the day the sanctions took effect, and several days later.More news: 'Happiness, Couple Fulfillment Ministry' was a typographical error - Okorocha
KT McFarland, a top official on President Donald Trump's transition team, said in an email last December that they should reassure Russian Federation, which she said had just "thrown the United States of America election" to Trump.
K.T. McFarland's nomination for US ambassador to Singapore is on hold.
Her written questions to the Senate Foreign Relations Committee did not acknowledge that conversation.
"On or about December 22, 2016, a very senior member of the Presidential Transition Team directed Flynn to contact officials from foreign governments, including Russian Federation, to learn where each government stood on the resolution and to influence those governments to delay the vote or defeat the resolution", the Justice Department's statement of offense against Flynn states.
Senior White House advisor Jared Kushner has said peace between Israel and Palestine was "achievable", although he added that the agreement should come from the countries of the region and not something imposed by the US.More news: Luxury Retailer Disdainful of Amazon Wins Appeal
Flynn then briefed senior transition team members about his discussions with Mr Kislyak, the records show.
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