The Mets have apologized to Newsday’s Tim Healey for Sunday’s postgame clubhouse incident at Wrigley Field, where Jason Vargas physically threatened Healey and manager Mickey Callaway told the team’s PR staff to remove the reporter during an obscenity-laced tirade.

“Jeff Wilpon called me [Sunday] evening to apologize on behalf of the organization,” Healey said during a telephone interview. “He stressed the fact that I should feel comfortable being able to do my job at the ballpark and that moving forward, there’s no reason for me to feel uncomfortable. I appreciated that sentiment from him, absolutely.”

The team also issued an email statement later Sunday night, mentioning the apology and pledging “further discussions” with the people involved. The Mets are expected to have general manager Brodie Van Wagenen join the Mets in Philadelphia for Monday’s opener of a four-game series against the Phillies.

“The Mets sincerely regret the incident that took place with one of our beat writers following today’s game in the clubhouse,” the statement said. “We do not condone this type of behavior from any employee.”

Callaway and Vargas took issue with Healey only minutes apart after the Mets’ 5-3 loss to the Cubs, who rallied to win on Javier Baez’s three-run homer off Seth Lugo in the eighth inning. With the team’s bullpen troubles a season-long concern, Callaway was peppered with questions from reporters regarding the decision to stick with Lugo rather than use closer Edwin Diaz earlier than the ninth, and after the testy exchange wrapped up, Healey headed to the main part of the clubhouse with the other reporters.

“Mickey came out of his office, dressed, and I thought he was leaving for the day, so I said, ‘See you tomorrow, Mickey,’ ” Healey said. “And then he said, ‘Don’t be a smart-ass.”

Healey said he was told by other reporters that Callaway continued to curse at him. Healey said he did not hear that because he was “10 feet away at that point.”

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Healey said Callaway then went into another room, and when the manager returned after a few minutes, he picked up where he left off.

“I couldn’t confidently tell you exactly what he said, but he said, ‘You know we’re going to be in a bad mood after a loss,’ or something like that. And I tried to tell him, I didn’t mean anything by it. I was just saying I’ll see you tomorrow. And then he said, ‘Get this guy out of here,’ and that got the attention of Jason Vargas.”

According to Healey, Vargas was getting dressed at his locker, which was about 15 feet away in the cramped visitors’ clubhouse, and Healey noticed the pitcher had been staring at him for what seemed like roughly 45 seconds. Healey said he was just standing there, “wondering why Mickey was blowing up,” when he saw Vargas. He recalled asking him if everything was OK or if there was something he wanted to say.

That’s when Vargas threatened him.

“He said, ‘I’ll knock you out right here’ and then took a couple of steps toward me,” Healey said. “Some people said charged — charged is super-strong.”

Mets media relations manager Ethan Wilson got between Healey and Vargas while other players, Noah Syndergaard and Carlos Gomez among them, moved in to make sure the pitcher remained at a distance. Healey said he walked away at that stage.

“I was shocked, and at the same time trying to tell Vargas or Callaway or Ethan, ‘Hey, I didn’t mean anything by it,’ which might have been interpreted as aggression on my part. I was in no way trying to be aggressive or antagonistic or anything. At that point in the day, I want to talk to Diaz and then leave, you know?

“What’s the point in me trying to pick a fight?”