U.S. agencies intercepted phone calls last year between Russian intelligence officials and members of Donald Trump's 2016 campaign team, conversations a Kremlin spokesman has denied, according to The New York Times.

The Times reported that the Russians made contact with Paul Manafort, who briefly served as Trump's campaign chairman. In late August, Manafort resigned from that job after disclosures by The Associated Press about his firm's covert lobbying on behalf of Ukraine's former pro-Russia governing party.

Manafort told NBC News Wednesday that he had "no contact knowingly with Russian intelligence officials."

"I don't think it's possible I could have even inadvertently had discussions with Russian officials," he said. "It's not like they wear badges. The story is not true."

Current and former U.S. officials interviewed by the Times declined to identify other Trump associates contacted by the Russians.

The anonymous officials told the Times they found no evidence that the Trump campaign was working with the Russians on hacking or other efforts to influence the election.

The report comes a day after U.S. National Security Adviser Michael Flynn resigned following reports he misled Vice President Mike Pence and other officials about his contacts with Russia.

Speaking to reporters in Moscow, Dmitry Peskov, spokesman for President Vladimir Putin, denied the reports of intercepted phone calls between Russian intelligence officials and members of Trump's presidential campaign and pointed to the anonymity of the sources, saying that the reports "are not based on any facts, do not point to actual facts."

Hillary Clinton officials responded to the allegations on Tuesday, calling it a "colossal scandal." Brian Fallon, press secretary for the Clinton campaign, wrote on Twitter: "Everything we suspected during the campaign is proving true. This is a colossal scandal."

Robby Mook, Clinton's campaign manager, wrote on Twitter: "I'd like the FBI to explain why they sent a letter about Clinton but not this."

NBC News has not confirmed the details in the report by The Times.

Trump blasted the media coverage, tweeting early Wednesday, "The fake news media is going crazy with their conspiracy theories and blind hatred. @MSNBC & @CNN are unwatchable. @foxandfriends is great!"

He followed up with another message: "This Russian connection non-sense is merely an attempt to cover-up the many mistakes made in Hillary Clinton's losing campaign."

"Information is being illegally given to the failing @nytimes & @washingtonpost by the intelligence community (NSA and FBI?).Just like Russia."