US President Donald Trump slammed the newspaper in a Tweet after the announcement, saying that "The New York Times is Fake News!!!"
The New York Times has come under fire after it published an editorial on June 3 from US Senator Tom Cotton, a Republican from Arkansas, titled "Send in the Troops." Cotton wrote that an "overwhelming show of force" would restore order after protests spread across the country, some of which turned violent.
The protests for racial justice first erupted 13 days ago after video footage emerged showing George Floyd, a 46-year old unarmed black man in handcuffs, lying face down on a Minneapolis street on May 25 as a white police officer knelt on his neck for nearly nine minutes.
"It's past time to support local law enforcement with federal authority," Cotton wrote.
Cotton re-tweeted Trump's Tweet calling the paper "Fake News."
The editor, James Bennet, will be replaced by Katie Kingsbury. Bennet had been the Editorial Page Editor since 2016. He had helped expand the range of voices the paper published and explore new formats, according to a note publisher A.G. Sulzberger sent to staff.
Cotton and Bennet could not be immediately reached for comment.
Jim Dao, a deputy in the paper's opinion section who oversees op-eds, is stepping off the masthead to move into a new role in the newsroom, according to the Times.
Before joining the New York Times as an editor, Bennet was the editor-in-chief of news magazine The Atlantic. He was in the running for the top job at The New York Times.
Earlier in his career, he was a reporter with the New York Times.
His resignation comes as newsrooms across the United States examine their own track record with diversity and sensitivity to issues to people of color.
On Saturday, the top editor of the Philadelphia Inquirer, Stan Wischnowski, resigned after employees walked out in protest over a headline "Buildings Matter, Too," on a story about the impact of civil unrest on property.