A senior editor at the New York Times has resigned amid a furious backlash over the newspaper’s publication of a controversial and unfiltered comment piece penned by a Republican senator.

The article by Tom Cotton, junior senator for Arkansas and a fierce ally of Donald Trump, titled Send in the Troops, called for the president to invoke the insurrection act of 1807 and use US military forces against citizens to quell unrest sparked by the death of George Floyd.

In the days following its publication on 3 June, numerous current and former Times journalists criticised the decision to run it and the newspaper added a note to the essay on 5 June conceding it “fell short of our standards and should not have been published”.

On Sunday, the Times announced that James Bennet, its editorial page director since May 2016, had resigned with immediate effect, and that one of his deputy editors, Jim Dao, had been reassigned to the newsroom. 

The announcement gave no explanation for Bennet’s resignation or Dao’s transfer, but the news drew swift comment from Trump, who tweeted that the opinion editor had “quit over the excellent Op-Ed penned by our great Senator @TomCottonAR. 

“The New York Times is fake news,” the president added, repeating a familiar claim.

Cotton also weighed in, accusing the Times of lying and smearing his character. Cotton claimed he had not called for troops to be used against protesters but should be called on as a back-up “only if police are overwhelmed”.

Earlier in the day, Cotton blasted Bennet and the Times for reversing their initial decision to defend publication of the column in the aftermath of the staff revolt.

“The New York Times editorial page editor and owner defended it in public statements but then they totally surrendered to a woke child mob from their own newsroom that apparently gets triggered if they’re presented with any opinion contrary to their own, as opposed to telling the woke children in their newsroom this is the workplace, not a social justice seminar on campus,” Cotton fumed in an interview on Fox News Sunday.

Sewell Chan, a former NY Times editorial page director, was among those who spoke out against his former employers for running the article in the first place.

“The decision to publish [Cotton] calling for troop deployments to quell unrest falls short of sound journalistic practice,” he tweeted.

Nikole Hannah-Jones, a black New York Times magazine writer, said she was “deeply ashamed” of the newspaper in a tweet that amassed almost 120,000 likes.

The New York Times publisher AG Sulzberger acknowledged the turmoil in an internal memo sent to Times staff on Sunday.

“While this has been a painful week across the company, it has sparked urgent and important conversations,” Sulzberger wrote in the memo, reported by CNN.

“Last week we saw a significant breakdown in our editing processes, not the first we’ve experienced in recent years. James and I agreed that it would take a new team to lead the department through a period of considerable change.”

Those changes include an expansion of the newspaper’s fact-checking procedures and a reduction in the number of opinion pieces written by non-staff members, AP reported. 

Kathleen Kingsbury, another deputy editorial page editor who won a Pulitzer Prize for editorial writing at the Boston Globe before joining the NY Times in 2017, will take over Bennet’s role until at least the November presidential election, the statement said.

It’s not the first time the paper has faced backlash over a controversial op-ed. Earlier this year readers and staff spoke out against a piece published by the columnist Bret Stephens that critics said embraced eugenics.

The protest at the newspaper came as staff at the Philadelphia Inquirer called in sick over the newspaper’s decision to use the headline Buildings Matter, Too on an architecture article, a choice considered tone deaf and insensitive to the Black Lives Matter movement. The Inquirer has since apologized for a “horribly wrong” decision.