Several senior officials told CNN they were surprised by the criticism, and believe it could potentially jeopardize Whitaker's chances of remaining in the post if it continues to dominate headlines.
During a brief stint previous year as a conservative legal commentator on CNN, Whitaker often appeared as a Trump defender, saying he saw no evidence the president colluded with Russians during the 2016 campaign or obstructed justice.
The headline on the op-ed: "Mueller's investigation of Trump is going too far".
Trump abruptly altered the chain of command above Mueller on Wednesday, putting his work under the supervision of a Republican loyalist who has been openly skeptical of the special counsel's authority and has mused about ways to curtail his power.
In July 2017, before joining the Justice Department, Whitaker said during an interview on CNN that he could envision a scenario in which an acting attorney general doesn't fire Mueller but "just reduces his budget to so low that his investigations grind to nearly a halt".
President Trump and acting attorney general Matt Whitaker. They were aimed at protesting the ouster of Sessions, whose recusal allowed Mueller to operate unimpeded, and as a warning that Whitaker should not interfere with the investigation. The special counsel's team has been investigating Stone's connection to WikiLeaks during the 2016 campaign and whether he had advance knowledge of the group's plans to release hacked material damaging to Democrat Hillary Clinton.
Whitaker's stances on the Robert Mueller probe and a number of other hot-button topics have drawn criticism. During a 2014 debate in Iowa when he ran for the Republican nomination for USA senate, Whitaker reportedly said he'd like to see federal judicial nominees be "people of faith" with a "biblical view of justice". Christie also oversaw the transition process before Trump took office.
"There is a very specific scope to this investigation", Whitaker said.
Protesters held signs reading: "Putin/Trump Make Russia Great Again", "Just when you thought things couldn't get any worse", and "Only guilty men fear the truth".
Whitaker also laid out in a July 26, 2017, CNN appearance a hypothetical scenario in which Mueller's investigation could be stifled without him being fired.
In a statement Thursday, the Republican said Whitaker is a "steady hand that will provide good leadership and judgment, and will ensure that the United States Department of Justice upholds the highest standards of the rule of law".
On Thursday, two people close to Whitaker said he has no intention of taking himself off the Russian Federation case.
"There was interference by the Russians into the election, but that was not collusion with the campaign", Whitaker said on "The Wilkow Majority". "That's where the left seems to be combining those two issues".