Clemens, 45, was officially scratched from his scheduled start against the Devil Rays on Tuesday because his tweaked left hamstring may still not be strong enough to hold up to pitching in a Major League game, particularly covering bases on ground balls.
While the Yankees completed their home schedule against the Blue Jays on Monday, Clemens was working out at the club's Minor League complex on Himes Avenue in Tampa, throwing off a mound and long-tossing across an outfield. The results were not satisfactory enough for club brass to sign off on Clemens' return to the rotation.
"We had told him before he left [New York] that if there was any kind of hesitation or anything that we would have to make an adjustment for, we would do it," Yankees manager Joe Torre said. "He feels it a little bit."
Clemens called general manager Brian Cashman in the second inning of New York's 4-1 loss to report that while he believed he could pitch if necessary, the hamstring was drawing concern. Officials in attendance agreed with the right-hander's self-analysis.
"I think at the beginning, they liked what they saw," Clemens said. "Near the end, they didn't. I still think it would have been an issue to try and cover a base or [make] a quick movement here or there.
"I still think it's improving every day. I'm just listening to what our trainers are saying. I've got a little swelling, but I ran quite a bit in the deep end of a pool to try and get that motion going. I'm really going to try."
Clemens, who is 6-6 with a 4.18 ERA in 18 games (17 starts) for the Yankees, made just two starts in an injury-plagued September. Clemens had two cortisone shots administered in his pitching elbow due to ligament damage, and he also endured bleeding blisters in his right foot in addition to the hamstring injury, which he suffered while running last Thursday.
Cashman said that while Clemens' injuries were enough of a concern to make it an easy decision to remove him from the rotation, they would not have precluded him from pitching in a must-win contest or a postseason game. Entering play on Tuesday, the Yankees' magic number to clinch a playoff spot was at one with six games remaining.
"I think the right moves are being made, to give him more time," Cashman said. "We're just playing it smart and looking at the big picture. ... If today's game was the last game of the season and we were in this same situation, nothing would stop him from pitching and giving it everything he had."
Clemens said that he feels confident he will be available in October.
"I fully expect to be out there," Clemens said. "From where this team started and where we are now, it's been incredible. That's another reason why I'm happy for all these guys. For how the team started to now, a lot of guys should be proud of these guys."
Left-hander Kei Igawa was inserted as New York's starting pitcher on Tuesday as the club prepared to open a three-game series at Tropicana Field. Igawa last pitched in relief on Saturday against the Blue Jays, recording one out. He had not started a Major League game since July 26 at Kansas City.
Clemens said that he had been hoping to make at least one more start before the conclusion of the regular season, but Torre said that the club would instead prefer that he pitch in a simulated game so that the conditions could be controlled. As Torre said, Clemens could stop from covering first base in a simulated game if his hamstring gave him trouble; in a Major League contest, Clemens would be a risk to run until it blew out.
"I'm going to find a way to get the work that I need," Clemens said. "I was holding on to a regular-season start as long as possible because I just wanted to do it. I'm just going to do everything they tell me to do."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.