Johan Santana's comeback from shoulder surgery has stalled.

The New York Mets ace was scratched from his next scheduled rehab start because of lingering discomfort in his pitching shoulder. He will head back to New York to be examined by a doctor Thursday and it's uncertain if he will get back to the majors this season.

"I don't really believe this is about this year. This is about a timetable that will get him ready and if part of that timetable is pitching games in the major leagues this year, good. If it's not, it's not," general manager Sandy Alderson said Tuesday. "We're certainly not going to rush things. I think right now a window in September is open to us. If it closes, that's the way it goes."

Santana pitched three scoreless innings last Thursday for Class-A St. Lucie in his first rehab outing since undergoing surgery last September to repair a torn anterior capsule in his left shoulder.

The two-time Cy Young Award winner was slated to pitch again Wednesday for St. Lucie, but Alderson said Monday that Santana would likely be pushed back a day because he didn't feel as strong as he wanted to following the first outing.

Then, on Tuesday, Alderson said the 32-year-old left-hander was scheduled to see the doctor and won't pitch again until at least next week.

"There is some lingering discomfort in his shoulder and we want to make sure that's checked out before we go any further with the rehab," Alderson said. "I can't comment on the severity of this discomfort — that's one of the reasons we want him seen by a doctor — but there is some there. More than anything else, Johan would like to have it checked out before he proceeds."

Alderson said he wasn't sure whether the news should be characterized as a setback for Santana, but it definitely delays his rehab schedule.

"I wouldn't say this is something we expected, but in the overall course of things, it's probably not something that should be unexpected," Alderson said.

"Nothing is worth it to the point where we're going to push him to do something that he's not capable of doing. I've already said that as far as 2011 is concerned, we're not looking for him to contribute to a pennant race, so we will view September as part of his overall recovery from this surgery. If he's able to pitch, great. If not, we'll work that into his offseason schedule and spring training."

Santana threw 26 of 33 pitches for strikes and allowed two hits last week against the Daytona Cubs. He played long toss after the outing but did not throw a bullpen session, Alderson said.

Acquired from Minnesota before the 2008 season, Santana is signed through 2013 on a deal that guaranteed him $137.5 million over six years.