After Mets third baseman David Wright was hit in the head by a 94 mph fastball last weekend, causing a concussion, Manuel said Wright was a "different animal" than Church, who missed much of last season with New York following a pair of concussions.
Church, traded to the Atlanta Braves last month, took exception to that, inferring that Manuel was questioning his toughness.
"It just felt like a low blow," Church said. "I saw it. I wasn't happy. If he had a problem with me or anything like that, you'd think he'd tell it to my face. I had plenty of opportunity to talk while I was wearing that uniform. It just was like, all right, now that I'm wearing another one, why would he come out and say that?"
When he met with reporters before Tuesday night's series opener against the Braves, Manuel was told that Church called the comments a "cheap shot."
But Manuel said he meant no disrespect. He said he was simply trying to explain that the players involved were different, just like the concussions.
"There's no ill intent," Manuel said. "I don't mean to take a shot at him. If that's how he felt, I apologize to him. I like Ryan Church."
Church contacted Wright to offer advice and support to his former teammate soon after Wright was nailed on the head
by Giants pitcher Matt Cain.
"That's what I told him: 'Don't be a hero,' " Church said.
Wright said he appreciated the gesture and was encouraged that he hadn't experienced many of the symptoms that troubled Church, such as nausea and sensitivity to light. Wright was placed on the 15-day DL the day after he was beaned, even though he lobbied team executives not to make the move.
The Mets might be learning from their experience with Church, who suffered his first concussion March 1, 2008, during spring training, when he collided with teammate Marlon Anderson.
Church's next concussion happened on May 20, when he took an accidental knee to the head in Atlanta while sliding into second base trying to break up a game-ending double play.
The Mets have been criticized for rushing Church back. He was used as a pinch hitter two days later and didn't go on the disabled list until June 10. In the meantime, he endured a miserable flight with the team to Colorado and its thin air, exacerbating his post-concussion symptoms.
He came off the disabled list June 29, then went back on from July 8 to Aug. 22.
Why did Church keep playing? He wanted to help his club, which collapsed in September and missed the playoffs for the second consecutive season. When asked by the Mets whether he was OK, Church said his normal response was, "I'm good."
He said that sort of stubborn attitude is in a ballplayer's DNA.
"From the outside looking in, the smartest thing to do obviously was to go on [the DL]. But for me, I was trying to just get back and play. I mean, they were telling me if I would have went out there and got another one, my career would have been over. And that didn't really sink in. And it wasn't like anybody was telling me, no, don't do it, go on the DL," Church said.
Looking back now, he knows it was unwise.
"I would be trying not to throw up. Standing in the outfield, just spinning like no other. Just trying to take those deep breaths, like just trying to relax myself, don't get all panicky," Church said. "It went on and off the whole year, but mostly the bad stuff was when I first came back. It was way too soon."
Manuel and Church appeared to have had a strained relationship during the outfielder's 1½ seasons in New York, though they both disputed that perception publicly.
Manuel said the two didn't communicate very well about Church's concussions.
"We didn't have clarity on the message that we were getting from him," Manuel said. "I'm as much to blame as he is."
Church said he doesn't blame the Mets for how they handled his injury, and he's ready to move on.
"It was a whole learning process. We all went through it," Church said. "I'm just thankful that I can still play."
In other news, the Mets announced that they signed their top draft pick, left-hander Steven Matz from nearby Ward Melville High School on Long Island, about an hour's drive from Citi Field.
The club gave Matz, selected No. 72 overall, an $895,000 signing bonus.
The 6-foot-3, 195-pound Matz grew up a Mets fan and will report to the rookie-level Gulf Coast Mets in Florida. He was at Citi the ballpark with his parents and spoke with reporters in New York's dugout, sitting on the bench next to general manager Omar Minaya and amateur scouting director Rudy Terrasas.
"It's like surreal," Matz said. "It's really starting to set in now."
Minaya said the deal got done only a couple minutes before the midnight deadline Tuesday morning.
Cora was placed on the 15-day disabled list, retroactive to Thursday, for the second time this season. He is scheduled to have surgery on his right thumb Thursday. Five weeks later, he'll get his left thumb fixed. Both need ligament repairs.
The move means the depleted Mets have used the disabled list 20 times (among 18 players) this season, most of any major league team, according to the commissioner's office.
Information from The Associated Press was used in this report.