In separate interviews on Monday, the National Institute of Allergy and Infectious Diseases director argued that the US president’s campaign was "in effect, harassing me,” and should take down the commercial.
He told the DailyBeast that another advert would be “outrageous” and “terrible”, and warned that “their harassment of me might have the opposite effect of turning some voters off".
Dr Fauci, who advises the White House coronavirus task force, alleged on Sunday that the Trump campaign acted without his permission.
He also complained that his words had been taken “out of context” in the 30-second ad, which touted Mr Trump’s personal experience with Covid-19 and appeared to show Dr Fauci’s praise.
The sentence in question — “I can’t imagine that anybody could be doing more” — had been in response to the broader response of the Trump administration, Dr Fauci has claimed, and was not about the president.
“I was totally surprised,” he said in a statement that CNN reported. “The use of my name and my words by the GOP campaign was done without my permission, and the actual words themselves were taken out of context, based on something that I said months ago regarding the entire effort of the task force.”
The 79-year-old diseases expert, who has never publicly endorsed a presidential candidate, told CNN’s Jake Tapper on Monday "It's so clear that I'm not a political person".
"I have never —either directly or indirectly — endorsed a political candidate,” he argued. “To take a completely out of context statement and put it in which is obviously a political campaign ad, I thought was really very disappointing."
Dr Deborah Birx, the head of the White House coronavirus task force, told The Associated Press in an interview that "public health is not a political issue”, as she commented on the president’s attempt to include Dr Fauci in his campaign material.
According to a Kaiser Family Foundation poll last month, some 68 per cent of Americans said they trusted Dr Fauci to provide reliable information on the coronavirus, compared to 40 per cent for Mr Trump and 52 per cent for Mr Biden, the Democratic presidential nominee.
The Trump campaign, in response, has stressed that the comments are Dr Fauci's "own words".
"The words spoken are accurate, and directly from Dr. Fauci's mouth," said Trump campaign spokeswoman Erin Perrine.
Asked what his opinion would be of another campaign ad featuring his remarks, Dr Fauci told CNN: “You know, that would be terrible.
“That would be outrageous if they do that. In fact, that might actually come back to backfire on them.”