"I think that might be excessive," Paul said in an interview with "Kilmeade and Friends" first surfaced by CNN's KFILE.
Paul said that Republicans will "never even get started" with major policy changes like repealing Obamacare if they are focused on investigating their colleagues.
"I just don't think it's useful to be doing investigation after investigation, particularly of your own party. We'll never even get started with doing the things we need to do, like repealing Obamacare, if we're spending our whole time having Republicans investigate Republicans. I think it makes no sense," Paul said.
He said that President Donald Trump has apparently "handled the situation," unless there is further evidence of wrongdoing on Flynn's part.
"Unless there's some kind of other evidence of malfeasance, this sounds like something that was internal White House politics," Paul said.
Flynn resigned from his post late Monday, days after reports revealed that he spoke about sanctions with Sergey Kislyak, Russia's ambassador to the United States, on a call before Trump took office. This contradicted members of Trump's administration, including Vice President Mike Pence, who previously denied that Flynn and Kislyak discussed sanctions.
Sen. Roy Blunt (R-MO) told KTRS radio on Tuesday that the Senate Intelligence Committee should ask Flynn about his conversations with Kislyak.
"I think everybody needs that investigation to happen," he said. "I think that we should look into it exhaustively."
Speaking to reporters later Tuesday, Senate Majority Leader Mitch McConnell (R-KY) said it is "highly likely" that the Senate Intelligence Committee will investigate Flynn.
"The Intelligence Committee is already looking at Russian involvement in our election," he said. "They have broad jurisdiction over the intel community writ large."