New York Times executive editor Dean Baquet doesn’t have much respect for Project Veritas, but there’s little doubt that the undercover watchdog group is getting under his skin.

Mr. Baquet has blasted Project Veritas twice at recent forums, calling its work “dishonest” and “destructive,” even as the venerable left-leaning newspaper undergoes changes apparently spurred by founder James O’Keefe’s latest undercover sting on media bias.

The newspaper announced Oct. 13 that it had tightened its social-media policy, three days after Project Veritas released the first of four hidden-camera videos showing two New York Times staffers on hidden camera making their animosity toward President Trump clear.

What’s more, one of the employees, Times audience strategy editor Nicholas Dudich, may have resigned or been fired, given that his name has been removed the company directory, according to Mr. O’Keefe.

“The evidence suggests that Dudich does not work for The New York Times any more. Dean Baquet it seems may have fired Nick Dudich for telling the truth,” said Mr. O’Keefe in a follow-up video. “It seems as though telling lies gets you promoted at The New York Times while telling the truth gets you fired.”

In an Oct. 12 interview on TimesTalks, Mr. Baquet denounced Project Veritas for targeting a “young guy,” calling it “despicable,” but also said that the 28-year-old Mr. Dudich’s statements were “damaging” and that “we will deal with that.”

Mr. Dudich “made all kinds of outlandish claims. He was a kid. What James O’Keefe did in jeopardizing that kid’s career was awful,” said Mr. Baquet.

The other Times employee, London-based senior staff editor Des Shoe, is still listed on the newspaper’s website, although she has not written an article since Oct. 11.

That might have been the end of it, except that Mr. Baquet addressed the issue again during an Oct. 16 “Kalb Report” discussion on C-SPAN, slamming Mr. O’Keefe as a “conservative who goes out and tries to trick journalists into saying inappropriate things.”

Asked whether the Project Veritas “America Pravda” investigation should be considered journalism, Mr. Baquet said, “I don’t think it’s journalism, I think it’s destructive. It’s dishonest.”

“A journalist has to have at his heart or her heart a desire to make society better,” Mr. Baquet said. “All James O’Keefe is trying to do is hurt institutions and get some clicks.”

Mr. O’Keefe fired back with another video posted Oct. 25 defending the hidden-camera investigations, which he described as in the tradition of muckraking journalist Clarence Jones.

“Dean Baquet, since you’ve assigned motive to my heart, let me actually speak to our motivations,” Mr. O’Keefe said. “For us, it’s not about clicks. But your paper and your business model is about clicks. One of your senior editors was on our tape saying as much, saying it’s about a Trump bump and it’s about feeding readers what they want to read.”

He cited Ms. Shoe’s statement that newspaper subscriptions have “skyrocketed” as a result of the “Trump bump.”

“Let me actually define journalism, Dean Baquet,” said Mr. O’Keefe. “Journalism is about exposing the world for what it is, and it’s the discrepancy between how the world is and how it’s presented by the mainstream media that provides motivation for people like me to go out and do investigative reporting.”

Since founding Project Veritas in 2010, Mr. O’Keefe has touched off debate over whether going undercover is a legitimate journalistic practice, given that reporters must deceive others in their effort to get at the truth.

Such reporting has fallen off precipitously since the landmark Mirage Tavern story, a 1978 Chicago Sun-Times series in which reporters set up a fake bar in order to expose city corruption and shakedowns of local businesses.

Tribune Co. president Jack Fuller later said that the 25-part series failed to win the Pulitzer Prize because then-Washington Post executive editor Ben Bradlee raised objections over the deception involved.

“This put a damper on undercover investigation by news organizations,” said a post on the Pulitzer Prizes website. “By the time Fuller wrote his book in 1996, it had ‘gone out of fashion altogether.’”

Project Veritas has undertaken multiple undercover stings aimed at everything from exposing fraud to embarrassing politicians, but its American Pravda series is the first to take aim at the media.

Mr. Baquet said he was troubled by the Project Veritas deception as well as whether Mr. O’Keefe had the proper motivation.

“His employees lied about who they were,” Mr. Baquet said. “No, I don’t think that’s journalism. Journalism has got to have some value at its core, some desire to make society better or better informed, and that’s not that.”

The Times hasn’t always been so scrupulous about secretly obtained recordings. The newspaper ran the transcript of the 2012 Mother Jones undercover video showing Republican Mitt Romney alluding to the “47 percent,” as well as the 2016 Access Hollywood hidden audio in which Mr. Trump makes crass sexual comments.

Mr. Romney and Mr. Trump were public figures, unlike the Times employees, but Mr. O’Keefe chalked up the discrepancy to political bias.

“Baquet minimizes our journalism we think because our investigations don’t fit his biased narrative agenda. When Mother Jones released the famous 47 percent clip, the New York Times reported it without reservation,” said Mr. O’Keefe.

He noted in another video that the New York Times “recently embraced an investigation into the alt-right,” referring to a Sept. 19 op-ed about a Swedish student with the watchdog group Hope Not Hate who spent a year undercover.

Not all Times editors have been as willing as Mr. Baquet to take on Project Veritas. Mr. O’Keefe posted a video in which he tried to interview deputy managing editor Clifford Levy as he headed to and from a coffee shop.

Mr. Levy kept walking and said nothing.

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