Sean Spicer, Trump's spokesman, said Flynn and the Russian ambassador to Washington, Sergey Kislyak, aren't in frequent contact but they have been in touch recently on a number of issues.
Some instances included when the two had a conversation in the wake of the shooting of the Russian ambassador to Turkey, in which Flynn expressed his condolences, according to a transition official. The two men also exchanged holiday pleasantries via text message on Christmas, according to multiple transition officials.
The Russian ambassador texted Flynn on December 28 but the two did not connect by phone until December 29, according to a transition official.
A centuries-old law, the Logan Act, forbids any US citizen acting without official US authority from influencing "disputes or controversies" involving the US and a foreign government.
The December 29 phone call was on the same day that President Barack Obama ordered sanctions on Russia, as well as ordered 35 Russian diplomats and their families to leave the country -- but a transition official told CNN that Flynn and Kislyak did not discuss the Russian sanctions.
The Washington Post first reported
on the conversations.
Multiple transition officials, however, said that the call focused on the logistics of connecting Trump and Russian President Vladimir Putin after the inauguration for a phone conversation.
"The call centered around the logistics of setting up a call with the President of Russia and the President-elect after he was sworn in, and they exchanged the logistical information," Spicer said. "That was it. Plain and simple."
One of the officials added that Kislyak, in a conversation on December 29, also extended an invitation for a representative from the US to attend the upcoming Syria peace talks in Kazakhstan. The same day as that conversation, Russian Foreign Minister Sergey Lavrov made clear Trump would be welcome at the table for Syrian peace talks.
"I would like to express the hope that as soon as the administration of Donald Trump takes office, they will also be able to join these efforts," Lavrov said during a meeting with Putin in Moscow.
The Trump transition official said they are not aware of any additional conversations between Flynn and the Russian ambassador since December 29.
White House Press Secretary Josh Earnest was asked Friday whether it bothered the administration that Flynn was in contact with the Russian ambassador.
"I've read some of these reports and I think, to answer your question as bluntly as I can, it depends on what he said," Earnest responded. "And I know that some members of the President-elect's transition team have tried to describe those conversations. Obviously, I have zero insight into what may have been communicated back and forth, so I'd refer you to General Flynn himself or spokespeople for the transition who may be able to provide additional insight into the nature of those conversations and why those conversations were initiated."
Flynn's ties to Russia have been scrutinized since Trump tapped him to become his closest adviser on national security.
On one occasion, Flynn was seated next to Putin at a Russian media gala in December 2015, and he previously had a paid speaking gig with Russia Today, the Kremlin's TV network, though it was before he took on a formal campaign role.
On Friday, Trump again, using Twitter, denied claims that Russia had compromising information on him and continued to accuse the intelligence chiefs of leaking the allegations.