The daily said that the emails show Flynn was in touch with other transition team members before and after he spoke with Sergey Kislyak, the Russian Ambassador to the United States, about US sanctions against Russia.
"The emails directly contradict how the White House tried to portray Flynn -- as someone who acted alone," reported CNN.
It quoted the White House special counsel, Ty Cobb, as saying "after Flynn pleaded guilty Friday to lying to the FBI about his contacts with Kislyak: Nothing about the guilty plea or the charge implicates anyone other than Mr. Flynn."
A local media reported that one of the then-transition adviser, who later became deputy national security adviser under Flynn, in an email said that the sanctions against Russia were made to discredit Donald Trump's victory in the elections.
She said that the sanctions against Russia were meant to "lure Trump in trap of saying something" in defense of Russia, and were aimed at "discrediting Trump's victory by saying it was due to Russian interference".
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"As part of the outreach to Russia, she wrote that Flynn would speak to the Russian Ambassador to the United States Sergey Kislyak," said a daily.
United States President Donald Trump came in defence of Flynn, who pleaded guilty on Friday to lying to the FBI about his interactions with Russia, by stating that there was "nothing to hide".
The US President tweeted, "I had to fire General Flynn because he lied to the Vice President and the FBI. He has pled guilty to those lies. It is a shame because his actions during the transition were lawful. There was nothing to hide!"
According to reports, on being questioned if he was worried about what Flynn might say, the President said, "No, I'm not. And what has been shown is no collusion. No collusion. There has been absolutely no collusion. So we're very happy."
Flynn's plea agreement suggests that he provided information to prosecutors, which may help advance the inquiry.
He is accused of falsely telling the FBI that he did not ask Kislyak to "refrain from escalating the situation in response to [the] sanctions."
He was forced to resign in February after misleading the White House about meeting the Russian ambassador before Trump took office.
Flynn is at the center of a broader investigation by special counsel Robert Mueller into the Russian meddling in the 2016 US Presidential election campaign.
Apparently, Mueller's team was seeking a deal of some kind to win Flynn's cooperation in that investigation.