Concerns about questionable ties between the Donald Trump team and the Russian government continue to cast a shadow over the new administration, as Trump's pick for National Security Advisor, Lt. Gen. Michael Flynn, has reportedly been investigated by the intelligence community — including organizations which Flynn will now be overseeing in his new post.

The Wall Street Journal has confirmed that the U.S. intelligence community has investigated communications between Trump’s National Security Advisor Lt. Gen. Michael Flynn and Russian officials:

U.S. counterintelligence agents have investigated communications that President Donald Trump’s national security adviser had with Russian officials, according to people familiar with the matter.

Michael Flynn is the first person inside the White House under Mr. Trump whose communications are known to have faced scrutiny as part of investigations by the Federal Bureau of Investigation, Central Intelligence Agency, National Security Agency and Treasury Department to determine the extent of Russian government contacts with people close to Mr. Trump.

It isn’t clear when the counterintelligence inquiry began, whether it produced any incriminating evidence or if it is continuing. Mr. Flynn, a retired general who became national security adviser with Mr. Trump’s inauguration, plays a key role in setting U.S. policy toward Russia.

The news about Flynn’s numerous contacts with Russian Ambassador Sergei Kislyak raised serious concerns about whether or not Flynn had violated U.S. federal law and compromised national security. The report by the WSJ is the first confirmation that these concerns have been officially investigated.

As initially reported by David Ignatius in the Washington Post, Flynn communicated with Kislyak multiple times via text and telephone on December 28th and 29th. Notably, December 29th was the day then-President Obama announced sanctions against Russia for their interference in the U.S. presidential elections.

In response to the initial report of the contacts, Trump’s surrogate, and now Press Secretary, Sean Spicer tried to downplay the communications, citing only one call and claiming the discussion was about “logistics of setting up a call with the President of Russia and the President-elect after he was sworn in.”

In a phone call with journalists, representatives from the Russian Embassy declined to comment and referred to Flynn as one of a number of “local interlocutors:”

Questions about Flynn’s connections with Russia have persisted since he joined the Trump campaign as an advisor. Flynn was reportedly pushed out of his position with the Defense Intelligence Agency, leading to his retirement from the U.S. military. Flynn later entered into a relationship with Russia Today (RT), a broadcast outlet owned and run by the Russian government to disseminate propaganda in English. Flynn confirmed the relationship with RT was a paid one but evaded questions about the regularity of his engagement with them and falsely equated RT with CNN. As recently as 2015, Flynn gave a speech at an anniversary banquet for RT where he was photographed sitting at the literal right-hand of Russian President Vladimir Putin.

(Mikhail Klimentyev/Sputnik, Kremlin Pool Photo via AP, file)

The investigation of Flynn appears to be part of a larger inquiry by the FBI and five other intelligence agencies about ties between members of the Trump campaign team (and now, possibly, administration). The larger investigation reportedly includes exploration of whether funds from the Kremlin were used to aid Trump’s presidential campaign.

As the nominee for the position of National Security Advisor, Lt. Gen. Flynn was not subject to confirmation by the Senate. Flynn was sworn in yesterday, and as National Security Advisor, he now serves in a position overseeing the very organizations that investigated him, and that are still investigating the totality of troubling connections between Trump, his circle, and the Russian government.