Manager Charlie Manuel said Halladay had travelled to Los Angeles, where he was scheduled to be examined by Dr. Lewis Yocum on Tuesday.
"I'm sure he'll find out his problem tomorrow," said Manuel, noting he appreciated the pitcher's will to do his job despite the shoulder injury. "I've been around the game a long time and I never liked to tell someone I couldn't play. I played with a broken arm, I played with a whole lot of things. I got hit in the face and my lip was over my eye and I missed one day. ... Yeah, I understand that. He felt like he could go out there and still pitch. He wasn't thinking about pitching bad, he wanted to try. He's an upstanding guy, he's a straight guy. There should be more guys like that."
Halladay is 2-4 with an 8.65 ERA in seven starts this season after missing nearly two months last season — from late May to mid-July — with a strained right lat muscle.
He allowed nine runs in 2 1-3 innings against Miami on Sunday for his second straight loss and second outing in a row of less than four innings — third in all this year. The 35-year-old right-hander is in the final season of his contract, making $20 million this year.
Halladay said Sunday this is a new injury for him, and he started feeling discomfort the morning after an April 24 start against Pittsburgh. He has struggled his two times out since and has given up at least five earned runs in four of his seven outings this season.
Halladay was replaced on the roster by left-hander Joe Savery, recalled from Triple-A Lehigh Valley in time to join the club before the start of a three-game series in San Francisco.
"He's on our team and we'll use him when we have to," Manuel said.
Yet the Phillies hadn't decided how to cover what would have been Halladay's next turn to pitch, Friday at Arizona. Manuel didn't speak with Halladay on Sunday night during the team's cross-country trip, saying Halladay was sleeping when the skipper walked back to see him.
"I didn't want to wake him up," Manuel said.
Manuel is hopeful his club is better equipped to handle the loss of Halladay this season than a year ago, when the team struggled during his absence and wound up missing the playoffs for the first time in six years.
"If you look and you see our rotation and you our bullpen, the back end of our bullpen has been pretty consistent," Manuel said. "We've been inconsistent from the middle until we get to the eighth inning."
AP Sports Writer Rob Maaddi in Philadelphia contributed to this report.