Trump said this week he valued Fauci's input but did not always agree with him.
"You know, it is a bit bizarre. I don't really fully understand it," Fauci said in an interview with The Atlantic.
He said he believed the people involved in releasing that list, which was misleading because it did not include the entirety of Fauci's statements or other context, are really "taken aback by what a big mistake that was."
White House tensions with Fauci have risen with the decline of Trump’s popularity in opinion polls over the president’s handling of the outbreak.
The Republican president, who is seeking re-election in November, has been increasingly critical of government health officials and their guidance as a rise in infections threatens the easing of shutdown restrictions across the country.
Across the country, new cases are now averaging around 60,000 a day.
Before departing for a trip to Atlanta, Trump was asked whether Navarro had gone rogue.
"Well he made a statement representing himself. He shouldn't be doing that. No, I have a very good relationship with Anthony," Trump said.
Fauci told The Atlantic: "I can't explain Peter Navarro. He's in a world by himself. So I don't even want to go there."
Fauci said in a Financial Times interview last week he had not briefed Trump in two months.
He said on Wednesday his advice is passed onto Trump indirectly, via Vice President Mike Pence, who heads the White House coronavirus task force.
In his Atlantic interview, Fauci recommended the country hit a reset button and acknowledge that things are not going in the right direction.
The rising numbers of coronavirus infections show "we've got to do better" and states need to get on the same page and work on ways to control the virus.
"So, rather than these games people are playing, let's focus on that," Fauci said.
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