President Donald Trump may regret his criticism of the naming of a special counsel to take over the Russia probe, former FBI Assistant Director Chris Swecker told CNBC on Friday.

"I think it was a mistake," Swecker said on "Squawk Box," a day after Trump said he was the target of a "witch hunt" after the appointment of former FBI Director Robert Mueller to investigate alleged Russian interference in the 2016 election.

"Look, if there's nothing there, then he has absolute nothing to worry about. And I would — if he knew what I knew — applaud this. Because Director Mueller will keep this out of the press. He will make sure that this team is buttoned down, and not talking," he said.

On Wednesday, Justice Department officials announced that Deputy Attorney General Rod Rosenstein had tapped Mueller as special counsel.

At a White House lunch with reporters on Thursday, Trump was asked about the appointment of a special counsel.

"I believe it hurts our country terribly, because it shows we're a divided, mixed-up, not-unified country," Trump said. "And we have very important things to be doing right now, whether it's trade deals, whether it's military, whether it's stopping nuclear — all of the things that we discussed today. And I think this shows a very divided country."

Swecker said he opposed the appointment of a special counsel at first, but after witnessing the public perception of the Russian investigation, he thought it was time.

"Anything that comes out of his findings ... he's not going to go far afield. He's going to stick to his knitting. He's not going to go looking for dresses and scandalous things. He's going to stick to the facts," Swecker said.