They also provide the clearest picture yet of coordination between Flynn and other Trump advisers in contacting Russian officials to influence international policy.
The investigation of the contacts ahead of a United Nations Security Council vote on Israeli settlements could have implications for others involved, including Trump and his son-in-law and senior adviser, Jared Kushner.
Sources familiar with the matter told CNN that Kushner is the "very senior member"
of Trump's transition team who is mentioned in Friday's court filings
as having directed Flynn to contact the Russian ambassador to the United States Sergey Kislyak and other countries about the UN Security Council vote on the Israeli settlements.
Although they don't name any transition officialts, the court filings say a "very senior member" of Trump's transition team asked Flynn to contact officials from UN Security Council countries, including Russia, to learn where each country stood on the vote on a resolution condemning Israeli settlement activity.
A person familiar with the transition's effort on the UN resolution said it was well-known and a collaborative effort by various transition officials, including Reince Priebus, Steve Bannon, Flynn and Kushner, adding that none of them "ordered" or "directed" the others and all were working toward the same goal of standing by Israel.
An attorney for Kushner did not comment.
Before the vote, the Israeli government lobbied the Obama administration to kill the resolution, but the efforts fell flat. The Israeli government then reached out to the Trump transition
and asked for help in pressing for a veto of the resolution, a senior Israeli official told CNN at the time.
The resolution was originally proposed by Egypt. On December 22, Trump spoke with Egyptian President Abdel Fattah al-Sisi before the scheduled vote. After the call, Egypt withdrew the proposal, but other countries later stepped in to put it back on the docket.
Intelligence intercepts picked up Kushner's conversations with foreign intelligence targets about efforts to stop the Israeli settlements resolution, according an official briefed on the matter. In addition, communications intercepts captured Israeli officials saying that Kushner told them he would help with the resolution, a former senior US intelligence official tells CNN.
At President Barack Obama's direction, the US abstained from voting on the resolution, a rare move that allowed the UN Security Council to unanimously condemn Israeli's settlement activity. Israel was vehemently opposed to such a move by its closest ally and appeared to be lobbying the incoming president to change US policy. The Trump transition's offer to the Israelis to provide help would appear to violate the long-held principle that presidents-elect refrain from interfering in US foreign policy during the transition based on the idea that there is "only one president at a time."
The court filings on Friday also show that Flynn was working with other members of the Trump transition team when he spoke to Kislyak about US sanctions against Russia.
On December 28, Obama announced new US sanctions on Moscow in response to Russia's meddling during the 2016 election. The following day, Flynn spoke to a "senior official" on the transition team at Trump's Mar-a-Lago resort to discuss "what, if anything, to communicate to the Russian Ambassador about the US sanctions," according to the documents.
Former deputy national security adviser KT McFarland was the senior transition official at Mar-a-Lago who discussed with Flynn what to communicate to the Russian ambassador about US sanctions, according to sources familiar with the matter. McFarland was not named in the document, but sources confirmed she was one of the transition officials described in the court filings.
An attorney for McFarland declined comment.
McFarland met with Mueller investigators recently to answer questions about Flynn, the sources said.
According to the special counsel charges, McFarland and Flynn talked about the potential impact of the sanctions on the incoming Trump administration's foreign policy and that the transition team did not want Russia to escalate the situation.
Flynn then called Kislyak to request that "Russia not escalate the situation and only respond to the US sanctions in a reciprocal manner," according to the court documents.
After his call with Kislyak, Flynn briefed the transition team members about his conversations with the ambassador and Russia's decision not to escalate the situation.
Flynn lied to investigators about these calls with the ambassador, according to his guilty plea and the criminal statement of offense.
The charging document states that Flynn made a false statement to the FBI when he stated that in December 2016 he did not ask Kislyak "to refrain from escalating the situation in response to sanctions that the United States had imposed against Russia that same day; and Flynn did not recall the Russian ambassador subsequently telling him that Russia had chosen to moderate its response to those sanctions as a result of his request."
The document also says that Flynn falsely said he did not ask Kislyak to delay the vote on the UN Security Council resolution.
The White House said late Friday morning that "nothing about the guilty plea or the charge implicates anyone other than Mr. Flynn."
"The conclusion of this phase of the special counsel's work demonstrates again that the special counsel is moving with all deliberate speed and clears the way for a prompt and reasonable conclusion," Ty Cobb, a White House lawyer, said in a statement.