The warning was issued after seven players were hit by pitches when the teams met last week at Shea Stadium, including six Nationals.
Jose Guillen was plunked twice by Pedro Martinez, and the second time he slowly approached the mound, waving his bat, but was restrained. The tensions escalated after Guillen said things could get ugly if Martinez hit him again.
The warning gives the umpiring crew the discretion to eject a pitcher without warning if he feels a pitch was thrown with intent at a batter.
"They've always had that (authority)," Mets manager Willie Randolph said. "Your hands are tied. There's nothing you can do. You have no control over it."
REPLAY: Pedro Martinez is always the focal point in every game he pitches. It was that way in Wednesday night's 3-1 victory over the Nationals, a team he faced last week at Shea Stadium and hit three batters, including Jose Guillen twice.
Guillen threatened mayhem if he were hit again, and he had a chance to extract his revenge when he came up with the bases loaded and one out in the sixth.
Martinez fell behind 2-and-1 before getting Guillen to ground into an inning-ending double play.
The Mets ace got the win, allowing three hits and one run in seven innings.
RHP Victor Zambrano will make his first start of the season Thursday at Washington. Zambrano has been pushed back twice with tightness in his left hamstring and a bout with the flu.
C Ramon Castro could get a start behind the plate Thursday with Paul Lo Duca getting a rest.
2B Kaz Matsui went 0-for-3 with a walk in another extended spring training game. He could play in another game Thursday, and then play for Class A Port St. Lucie.
LHP Billy Wagner could be used in non-save situations for the next few days because he's rusty. Wagner missed over a week at the end of spring training with tightness in his left middle finger.
RHP Mike Pelfrey, the Mets' 2005 first-round pick, earned his first professional victory Tuesday night for Class A Port St. Lucie over Daytona. He gave up a run on four hits in six innings. GM Omar Minaya said there's no timetable for moving up to the next level.
Last year wasn't a good one for CF Carlos Beltran in his first season with the Mets after signing a seven-year, $119 million contract.
A strained right quad muscle in May and facial fractures sustained in an August collision with Mike Cameron contributed to Beltran's season in which he hit a very pedestrian .266 with 16 homers and 78 RBIs.
Beltran was booed Opening Day and for much of the first homestand when he was held hitless in his first nine at-bats.
His reception figures to be much better when the Mets return for their second homestand this weekend against the Brewers.
Beltran said he's more relaxed at the plate, as evidenced by a five-game stretch last week in which he hit two homers and drove in eight runs.
"I've been swinging the bat better," Beltran said. "I'm seeing the ball and getting a good swing on it."