"That's their prerogative -- we're confident of the facts as we presented them," said a team source who was unaware of MLB's plans to review Perez's medical records.
Before Saturday's game, manager Jerry Manuel was asked if he understood that there would be skepticism about the roster move and whether he thought it was warranted.
"This, purely, is Oliver Perez. Oliver Perez came in and said his knee is bothering him," Manuel said. "I've been [with the Mets] for a number of years and the integrity of those men [in the front office] has not wavered when it comes to these situations."
Perez, who is under contract to earn $12 million dollars this season, was removed from the Mets' starting rotation after failing to pitch into the fifth inning in consecutive starts on May 9 and 14. He was 0-3 with a 5.94 ERA at the time of the move to the bullpen.
Since then, Perez has pitched just 5 1/3 innings over four appearances, mostly in mop-up duty.
The Mets wanted to send Perez down to Triple-A to work on regaining his control and lost velocity on his fastball in hopes that more work would return him to form.
Perez has a stipulation in his contract that prevents the Mets from sending him down to the Minor Leagues without approval from Perez.
With Jonathon Niese coming off the DL Saturday, there was speculation that if Perez were to accept a Minor League assignment, this would be the time to do it.
By putting the 28-year-old on the DL, the Mets avoided having to make another roster move in the event Perez was still not willing to accept his assignment.
Manuel did not rule out the possibility that Perez had been pitching injured for all or most of the season.
"I thought that with the velocity not getting to where it was in 2008, that always concerns me," Manuel said. "But if the athlete tells you that he's fine, then he's fine. If he doesn't feel any pain, then you have to give him the benefit of the doubt."
Kyle Maistri is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.