Pelfrey's status for Sunday's game against the Brewers is uncertain after Tuesday's MRI revealed that he has right forearm tendinitis.
Manuel said that the team approached Pelfrey to have his arm checked out following his performance on Monday, in which he was relieved after allowing five earned runs and eight hits in five innings.
In his first two starts this season, Pelfrey has walked six batters, allowing nine earned runs in 10 innings en route to an 8.10 ERA.
Though Pelfrey downplayed the effects of his forearm on his pitching performance, Manuel reiterated on Thursday that the team will cautiously wait and see.
Pelfrey started taking anti-inflammatory medication on Wednesday and will combine rest with ice in the hopes of being 100 percent in "a few weeks."
But given that the season is young, the Mets may be more inclined to proceed with caution.
If Pelfrey doesn't start on Sunday, the Mets will call up someone from their farm system for a spot start.
Manuel did not name anyone specific, and when asked about Nelson Figueroa's two-inning appearance on Thursday for Triple-A Buffalo, said simply that the organization is taking necessary precautions.
"I don't know exactly what [Figueroa] did today, but I do know that the development system is going to give us every opportunity to make a choice," Manuel said. "So we will see what happens going forward."
Brittany Ghiroli is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.