"The Acting Attorney General is in charge of all matters under the purview of the Department of Justice," a spokeswoman for the department said Wednesday when asked if Whitaker would oversee Mueller's investigation.
Trump announced in a pair of tweets minutes earlier on Wednesday that Attorney General Jeff Sessions would be replaced by Whitaker, who was Sessions' chief of staff at the Justice Department. Sessions had resigned at Trump's "request," according to his resignation letter.
In a statement, Whitaker said he was "committed to leading a fair Department with the highest ethical standards":
"It is a true honor that the President has confidence in my ability to lead the Department of Justice as Acting Attorney General. I am committed to leading a fair Department with the highest ethical standards, that upholds the rule of law, and seeks justice for all Americans. I will work with our colleagues in Federal, State, local, and tribal leadership, including our partners in law enforcement and our U.S. Attorneys, to ensure the safety of all Americans and the security of the nation.
Attorney General Sessions has been a dedicated public servant for over 40 years. It has been a privilege to work under his leadership. He is a man of integrity who has served this nation well."
It was not immediately clear how the staffing change will impact Deputy Attorney General Rod Rosenstein, who is currently overseeing the Mueller probe. At about 3:45 p.m. ET, NBC reported that Rosenstein was headed to the White House for a "previously scheduled meeting."
Whitaker argued in an August 2017 op-ed for CNN that Mueller's investigation is "dangerously close to crossing" the so-called red line not to look into the Trump family's finances.
"It does not take a lawyer or even a former federal prosecutor like myself to conclude that investigating Donald Trump's finances or his family's finances falls completely outside of the realm of his 2016 campaign and allegations that the campaign coordinated with the Russian government or anyone else," Whitaker wrote in the piece.
"That goes beyond the scope of the appointment of the special counsel."
Less than a month earlier, Whitaker had defended Trump's son, Donald Trump Jr., for accepting a meeting at Trump Tower in June 2016 with Russian officials who had promised damaging information about Hillary Clinton during the presidential campaign.
"You would always take that meeting," Whitaker said on CNN.
Whitaker, 49, is a former U.S. attorney in Iowa who ran for political office as a Republican. The National Association of Former United States Attorneys announced in October 2017 that Whitaker had been appointed as Sessions' chief of staff.
In 2014, Whitaker chaired the Iowa State Treasurer campaign of Sam Clovis, who became a campaign aide for Trump in the 2016 election. Clovis had reportedly discussed Russian relations with George Papadopoulos, a Trump campaign foreign policy aide who pleaded guilty in October 2017 to lying to the FBI as part of the Mueller probe. Clovis has met with Mueller's team as well, The New York Times reported.
Reached by phone Wednesday, Clovis said, "I'm not gonna talk to you today, sorry," before hanging up.
Sessions had been a frequent target of Trump's ire since he recused himself from the investigation into Russian interference in the 2016 election and whether the Trump campaign colluded with the Kremlin.
Trump has also criticized Rosenstein. "I am being investigated for firing the FBI Director by the man who told me to fire the FBI Director!" Trump said in a June 2017 tweet, shortly after the special counsel was appointed.
The special counsel declined CNBC's request for comment on Sessions.
Sessions' resignation came less than 24 hours after most polls closed in the midterm elections. Democrats won majority control of the House of Representatives, while Republicans strengthened their hold on the Senate.
The announcement spurred an avalanche of statements from lawmakers of both major parties. Rep. Adam Schiff, D-Calif., who appears likely to become chairman of the House Intelligence Committee, said "Whitaker and any nominee must commit" to protecting Mueller and the independence of the Justice Department.
The timing is especially significant given that the new session of Congress with a Democrat-led House will not begin until Jan. 3, 2019.
We are "not likely to have any meaningful congressional oversight in the next 60 days," said William Heffernan, law professor at John Jay College of Criminal Justice.
When Democrats do assume control of the House, they will also take leadership positions in the House committees — including the House Judiciary Committee, where Rep. Jerrold Nadler, D-N.Y., currently serves as top Democrat.
He is expected to chair the committee, and Heffernan said that "at that point, Nadler will surely subpoena Whitaker."
In a statement Wednesday, Nadler urged immediate action. "The firing of Jeff Sessions will be investigated and people will be held accountable. This must begin immediately, and if not, then a Democratic Congress will make this a priority in January," Nadler said.
House minority leader Nancy Pelosi, D-Calif., called on Whitaker to recuse himself, citing "his record of threats to undermine & weaken the Russia investigation."