WASHINGTON >> Questions about the Trump administration’s ties to Russia are hardly going to disappear with the firing of national security adviser Michael Flynn. Investigations are underway, and more are likely by the new administration and on Capitol Hill.

U.S. agencies, including the FBI, have been probing Russian interference in the 2016 presidential election. And three congressional committees are conducting their own investigations that include looking at contacts between Russian officials and members of the Trump campaign and administration.

This isn’t the first time Trump has distanced himself from an adviser in light of a relationships with Moscow. In late August, Paul Manafort resigned as Trump’s campaign chairman after disclosures by The Associated Press about his firm’s covert lobbying on behalf of the former pro-Russian ruling political party in Ukraine.

The New York Times reported late Tuesday that members of Trump’s campaign, including Manafort, had repeated contacts with Russian intelligence officials during the year before the election. The U.S. knew about these contacts through phone records and intercepted calls, the Times said.

Reached late Tuesday, Manafort told The Associated Press he has not been interviewed by the FBI about these alleged contacts.

“I have never knowingly spoken to Russian intelligence officers and I have never been involved with anything to do with the Russian government or the Putin administration or any other issues under investigation today,” Manafort said.

Officials who spoke with the Times anonymously said they had not yet seen any evidence of the Trump campaign cooperating with the Russians on hacking or other attempts to influence the election.

Trump’s own ties to Russia have been questioned in light of his friendly posture toward the long-time U.S. adversary and reluctance to criticize President Vladimir Putin, even for Putin’s annexation of Ukraine’s Crimea region in 2014.

“This isn’t simply about a change in policy toward Russia, as the administration would like to portray. It’s what’s behind that change in policy,” said California Rep. Adam Schiff, the top Democrat on the House intelligence committee, one of the congressional bodies investigating. Schiff said there are continuing questions about the Trump campaign’s ties to Russia and whether anyone assisted Moscow in hacking.

“It’s not just that an administration official was caught lying. It’s that the national security adviser to the president was caught lying and on a matter of central importance. So this is big,” Schiff said.

The Obama administration said Russia interfered in the 2016 election with the goal of electing Trump. Trump has acknowledged that Russia hacked Democratic emails but denies it was to help him win.

The investigations and the unusual firing of the national security adviser just 24 days into his job have put Republicans in the awkward position of investigating the leader of their party. Senior GOP lawmakers continue to deny Democrats’ requests that an independent panel be established to carry out the Russia investigation. So the congressional probes are ultimately in the hands of the Republican chairmen, and the executive branch’s investigation has been overseen ultimately by Trump appointees.

On Tuesday, Republican leaders focused on the idea that Flynn misled Vice President Mike Pence about the nature of his contacts with the Russian ambassador — not on any questioning of the relationship between Flynn and the ambassador. Democrats say a key issue is whether Flynn broke diplomatic protocol and potentially the law by discussing U.S. sanctions with Moscow before Trump’s inauguration.

The Justice Department had warned the White House late last month that Flynn could be at risk for blackmail because of contradictions between his public depictions of the calls with the Russian ambassador and what intelligence officials knew about the conversations.

“You cannot have a national security adviser misleading the vice president and others,” said Republican House Speaker Paul Ryan of Wisconsin.

Daniel Jones, a former lead investigator on the Senate intelligence committee, said it’s important that Congress investigate Flynn’s ties to Russia and make sure that doesn’t get lost in a broader probe into Russia and the 2016 election.

“This is a checks-and-balances issue,” Jones said. “This shouldn’t be a political issue.”

On the other hand, California Rep. Devin Nunes, chairman of the House intelligence committee, said he was concerned Flynn’s rights were violated in the interception of his conversations with the Russian ambassador.

“I’m just shocked that nobody’s covering the real crime here,” Nunes said. “You have an American citizen who had his phone call recorded and then leaked to the media.”

Nunes said he intended to ask the FBI “what the hell’s going on here.”

The FBI has wide legal authority to eavesdrop on the conversations of foreign intelligence targets, including diplomats, inside the U.S.

Flynn did not concede any wrongdoing in his resignation letter, saying merely that he “inadvertently briefed the vice president elect and others with incomplete information regarding my phone calls with the Russian ambassador.”

Democratic Sen. Ron Wyden of Oregon, a member of the Senate intelligence committee which is already investigating Russia and the 2016 election, said Flynn’s resignation raises more questions.

For example, he said, there are open questions about how many conversations Flynn actually had with the Russians and whether other people knew he was having them.

While North Carolina Sen. Richard Burr, chairman of the Senate intelligence committee, said much of the panel’s investigation will occur behind closed doors, Wyden said he planned to push to make the findings and hearings public.

Republican Lindsey Graham, who is leading a Senate judiciary subcommittee investigation into Russia’s interference in the 2016 election, echoed Wyden’s concerns about whether Flynn was acting alone and without direction in his contacts. White House spokesman Sean Spicer said Trump did not direct Flynn to discuss U.S. sanctions with the Russians. “No, absolutely not,” Spicer said.

“I think most Americans have a right to know whether or not this was a General Flynn rogue maneuver, or was he basically speaking for somebody else in the White House,” Graham told CNN Tuesday.

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Associated Press writers Eric Tucker, Erica Werner, Richard Lardner, Chad Day and Deb Riechmann contributed to this report.