Tempers are flaring at Citi Field.

A tumultuous Mets season took another strange twist, with general manager Brodie Van Wagenen punctuating a heated meeting with the team’s coaching staff by throwing a chair, according to club sources.

The incident occurred following Friday’s 7-2 loss to the Phillies in which closer Edwin Diaz imploded in the ninth inning, allowing four runs in his latest meltdown.

An irate Van Wagenen assembled manager Mickey Callaway and the coaching staff in the coaches room immediately after the game, according to a source, and lashed out at the individuals present, bemoaning the fact Jacob deGrom’s strong performance had been wasted. Accompanying Van Wagenen at the meeting was assistant GM Allard Baird.

After ripping the coaches, according to a source, the usually mild-mannered Van Wagenen picked up a chair and threw it and told Callaway to go conduct his “f–king press conference.” Callaway provided no hint that anything was amiss as he met with reporters following the loss.

Van Wagenen, reached by phone before the Mets faced the Phillies on Saturday, wouldn’t confirm or deny the incident.

“We as a staff often meet with coaches and players throughout the course of the season,” Van Wagenen said. “I am not going to give the specifics to any of those meetings.”

That sentiment was echoed by Callaway.

“I think when we have private meetings, we’ll keep all that content in the room, for good reason,” the manager said before the Mets’ 6-5 win over the Phillies on Saturday.

Van Wagenen’s outburst was just the latest turbulence for a team that began play 10 games under .500 and holding just a 5.8 percent probability of reaching the postseason, according to Fangraphs.

Two weeks ago at Wrigley Field, Jason Vargas had to be restrained from going after a reporter who had agitated the pitcher following a Callaway outburst at the same writer. Callaway apologized to the reporter the following day in Philadelphia, but needed two press conferences because he excluded mention of the apology in the first. That same night The Post reported Van Wagenen had been responsible for ordering an in-game move on June 1, when the GM, according to sources, communicated with a member of the support staff and ordered deGrom removed from a game in which the right-hander had sustained a hip cramp. Callaway complied with the order and took the heat after the Mets bullpen imploded in a loss at Arizona.

Last month, Van Wagenen fired pitching coach Dave Eiland and bullpen coach Chuck Hernandez, citing the poor performance by the team’s relievers. Phil Regan and Ricky Bones were installed as interim pitching and bullpen coaches, respectively, but the changes haven’t improved the situation. Included was a four-game sweep in Philadelphia, in which the bullpen was responsible for three of the losses.

And then, after a relatively low-key week, Diaz was battered in Friday’s loss. It came just eight days after he had surrendered five runs in a walkoff loss in Philadelphia. The Mets closer, who arrived with Robinson Cano in the deal that sent prospects Jarred Kelenic and Justin Dunn to the Mariners, entered play 1-6 with a 5.67 ERA.

Callaway remains likely to survive the season, after receiving multiple votes of confidence from the GM, and a club source indicated it was also unlikely any further coaching changes would occur.

“It’s fantastic,” Callaway said about his relationship with Van Wagenen. “We’re both passionate guys that want to win.”

Van Wagenen, who before the season anointed the Mets as the team to beat in the division, has avoided reporters seeking answers about the direction of the club, but is expected to hold a press conference Friday, before the team opens the second half in Miami.

— additional reporting by Dan Martin