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(CNN) —  

Former acting Attorney General Matt Whitaker privately acknowledged Wednesday that he had raised concerns with his staff at the Justice Department about the scope of the Southern District of New York’s case against former Trump attorney Michael Cohen, according to House Judiciary Chairman Jerry Nadler and Republican aides.

Whitaker thought some of the campaign finance charges against Cohen were “specious,” pointing to the failed effort to prosecute former Sen. John Edwards on similar charges, according to GOP aides who were in the room during Whitaker’s closed-door interview with Judiciary Committee leaders on Wednesday. But the Republican aides said he did not speak to the US Attorney’s Office for the Southern District of New York about the case, instead saying he had internal discussions with Justice Department staff about his concerns.

Whitaker also did not deny talking with President Donald Trump about Cohen’s case, in which the President was implicated in two federal crimes involving hush-money payments to silence his alleged affairs, Nadler told reporters Wednesday. The GOP aides said Whitaker did not remember having any conversations with Trump about the Cohen probe, and he said he would have remembered any contentious exchanges with the President about the case.

“Unlike in the hearing room, Mr. Whitaker did not deny that the President called him to discuss the Michael Cohen case and personnel decisions of the Southern District,” Nadler said, referring to last month’s daylong public hearing with Whitaker.

One Justice Department official in the room for the interview adamantly disagreed with Nadler’s characterization of the conversation.

“Consistent with his prior testimony, Mr. Whitaker said that he couldn’t discuss private conversations with the President, didn’t recall any conversation similar to the reported ’lashing out’ one, and that the President never directed him to do anything to affect that investigation,” the official told CNN. “Moreover, Mr. Whitaker repeatedly made clear that during his tenure, the Department handled the Cohen case (and all other cases) consistent with established Department policies and free from any improper interference.”

The top Republican on the committee, Rep. Doug Collins of Georgia, also pushed back on Nadler’s comments Wednesday, downplaying what Whitaker had told the committee and saying there’s no evidence Whitaker discussed the Cohen case with the President

“If Mr. Nadler chooses to say by absence of what (Whitaker) didn’t say, if that’s the way he is interpreting it, then Mr. Nadler will have to answer to that,” Collins said.

The revelations raise questions about whether Whitaker was given the job – after Trump fired Attorney General Jeff Sessions last fall – because the President was looking to install a loyalist who could rein in the federal probes dogging his presidency.

Nadler said Whitaker also told the committee he was involved in conversations about Southern District of New York US Attorney Geoffrey Berman’s recusal in the Cohen case. But the GOP aides said they didn’t recall he was involved in any discussions about the recusal of Berman, who was appointed by Trump. One GOP aide said Whitaker told them, “You just don’t undo recusals.”

Nadler also said that Whitaker told the committee Wednesday that he discussed whether to fire one or more US attorneys.

Collins, however, said that the conversations were part of normal “personnel decisions” while Whitaker was atop the Justice Department, and there was nothing “nefarious” about those talks. He said Whitaker did not identify the attorneys who were under discussion about possible reassignment.

Whitaker met with Nadler and Collins privately in order to clarify his public testimony last month, but there was no transcript taken of the closed-door meeting. Nadler said Whitaker’s response about the Cohen case came following CNN reporting in December that Trump twice vented to Whitaker about federal prosecutors who referenced the President’s actions in crimes Cohen pleaded guilty to.

The New York Times also reported last month that Trump had also asked Whitaker whether he could put Berman back in charge of the Cohen case after he had recused.

In his public hearing, Whitaker denied that Trump had lashed out at him, and he would not say anything about his conversations with Trump about Cohen or the Southern District of New York.

Nadler and other Democrats have suggested Whitaker’s testimony could have been incorrect, and Nadler requested that Whitaker return to clarify his comments, which led to Wednesday’s closed-door session with Nadler and Collins.

Asked what it meant that Whitaker “did not deny,” the conversations, Nadler said: “Just what I said, he did not deny it, unlike in the hearing room.”

“He would not say no,” Nadler said when pressed further.

Collins said that Whitaker told the committee leaders he discussed the Cohen case with his own staff, but he did not have any conversations with the Southern District of New York about the scope or Berman’s recusal.

The Georgia Republican also said that Nadler told Whitaker that his fears Whitaker would interfere with the Mueller investigation while he was acting attorney general were not “borne out.”

This story has been updated with additional developments Thursday.

CNN’s Laura Jarrett and Pamela Brown contributed to this report.