"In my nearly five decades of public service, I have never publicly endorsed any political candidate," Fauci said in the statement. "The comments attributed to me without my permission in the GOP campaign ad were taken out of context from a broad statement I made months ago about the efforts of federal public health officials."
Despite Fauci's objections, officials from the Trump campaign told ABC News they plan to continue to air the ad.
"The video is from a nationally broadcast television interview in which Dr. Fauci was praising the work of the Trump Administration. The words spoken are accurate, and directly from Dr. Fauci's mouth," Trump campaign spokesman Tim Murtaugh said in a statement.
In a tweet Sunday evening, Trump said that the statements in the video "are indeed Dr. Fauci’s own words," adding that his administration has done a "'phenomenal' job, according to certain governors."
The U.S. leads the world with COVID-19 cases with more than 7,750,000, and deaths with over 214,000, according to data from the Center for Systems Science and Engineering at Johns Hopkins University.
Since March, the country's seven-day average for newly reported cases has more than doubled, from 19,418 to 47,946, according to the COVID tracking project. The seven-day average for newly reported deaths his risen from 500 to 694.
CNN first reported Fauci's reaction to the political ad Sunday afternoon.
The back-and-forth between Fauci and the administration is the latest in the increasingly tense relationship between the veteran medical expert and the president.
The president has frequently dismissed Fauci's advice and analysis since the pandemic began -- yet has at times cited Fauci to back up the administration's policies.
During the first presidential debate, Trump stated that Fauci said "masks are not good" before changing his stance. Fauci told ABC News that his initial concerns were mischaracterized.
"Anybody who has been listening to me over the last several months knows that a conversation does not go by where I do not strongly recommend that people wear masks," he said.
During an interview with CBS Radio on Friday, Fauci described the Sept. 26 White House event where Trump announced Amy Coney Barrett as his Supreme Court nominee as a "super-spreader event."
In addition to Trump, several administration members, GOP leaders and other VIPs, including the first lady, tested positive for the virus in the days following the event.
"It was in a situation where people were crowded together and were not wearing masks. So the data speak for themselves," Fauci said in the interview.