Amid the first hearing of the Jan. 6 committee on Capitol Hill, Benner suggested that in order to "combat" national security threats within the country, the solution was to target the voters of the former president.
However, the Times' Justice Department reporter later took down the tweets, claiming they were "unclearly worded."
The Times did not respond to Fox News' multiple requests for comment, including an inquiry about whether Benner deleted the tweets at the direction of the paper.
In the original tweets, Benner stressed that the Jan. 6 committee "underscores" what she indicated was the ongoing threat within the U.S.
"Today's #January6thSelectCommittee underscores the America's current, essential natsec dilemma: Work to combat legitimate national security threats now entails calling a politician’s supporters enemies of the state," Benner wrote.
Benner explained, "As Americans, we believe that state power should not be used to work against a political figure or a political party. But what happens if a politician seems to threaten the state? If the politician continues to do so out of office and his entire party supports that threat?"
The Times' DOJ reporter cast doubt that the Pelosi-appointed committee would resolve the "dilemma" since it remained "unresolved" following the Russia investigation and both impeachments of President Trump.
"That leaves it up to voters, making even more essential free, fair access to the polls," Benner concluded.
Benner's comments were slammed by critics.
"Absolutely amazing: the New York Times' Justice Department reporter says the US faces an ‘essential natsec dilemma’: namely, that Trump supporters are ‘enemies of the state’ and all of the GOP is a threat to the State. This is a reporter -- not an op-ed writer -- saying this," journalist Glenn Greenwald reacted. "Hearing anyone describe a traumatic and violent experience provoke emotions: even for police officers. That's what today is for. But the fixation on 1/6 is about exactly this: classifying Trump supporters as Enemies of the State for political gain & Security State power."
"Here we have an NYT reporter, channeling the views of the corrupt FBI and DOJ officials who leak to her, straight-up saying that your political opposition to the ruling regime makes you an enemy of the state by definition," The Federalist co-founder Sean Davis summarized.
"This is such a wildly extreme statement on so many levels, couched in the phony language of journalistic impartiality," journalist Michael Tracey slammed Benner's comments.
Rep. Jim Banks, R-Ind., who was initially set to serve on the Jan. 6 committee but was rejected by House Speaker Nancy Pelosi, D-Calif., appeared to be taken aback by Benner's tweets.
"That’s the best summary of the Biden Admin’s domestic national security strategy I’ve ever read," Banks wrote.
The Times did not respond to Fox News' inquiry as to whether or not Benner's tweets violated the paper's social media guidelines.