Halladay, who is attempting to rebound from an injury-plagued 2012 season, allowed seven runs in just 2 2/3 innings against the Detroit Tigers.
"He says he's healthy, he feels good and nothing's wrong with him," Manuel said. "It concerns me, but I've been in the game long enough that if nothing is wrong with him, just keep working with him.
Dubee blamed the results on Halladay's mechanics.
"I would say there's some concern, but most of it has to do with him having no tempo to his delivery," Dubee said. "Nuances to delivery, guys fight that all the time."
Halladay, who entered with a 2.16 ERA in his first three spring starts, yielded six hits and four walks against the Tigers. The two-time Cy Young Award winner, who struggled with shoulder weakness last season, claimed that "nothing hurts" after Tuesday's outing.
"The results aren't satisfying and that's obvious but the work we've done, there's a lot of progress being made," Halladay said. "I just felt lethargic. The good part is there's no soreness, nothing hurts. I'll trade that any day of the week feeling lethargic over being sore like last spring training where there were times you're hurt."
Halladay threw a perfect game, tossed a no-hitter in his first career postseason start, won a National League Cy Young Award and was 40-16 in his first two seasons in Philadelphia. But last year, he had his fewest wins (11) since 2004 and the second-worst ERA (4.49) in his career.
Given his problems last year, his age (35) and the amount of innings (2,687) he's accumulated in 15 seasons with Toronto and the Phillies, Halladay acknowledged he faces a tough challenge regaining his old form.
"There's definitely work to be done, adjustments to be made," Halladay said, adding he's increased the intensity of his workout program and threw an extra bullpen session between starts. "Being that it's spring training and there's so much to be worked on, so much to try and achieve at this point, I felt like it's more important to work on this stuff now and I'd rather have that (feeling) now."
Dubee wouldn't bet against the eight-time All-Star right-hander regaining his old form.
"His work ethic is still there, his desire is still there," Dubee said. "I'll take my chances."
Halladay is entering the final season of a $60 million, three-year contract extension he signed after being traded to the Phillies in December 2009. He has a vesting option for $20 million for 2014, but it's unlikely he'll reach it because he has to throw 258 2/3 innings.
"My goal is to get to where the season starts and I can maintain the strength level the entire season," Halladay said. "To do that, I have to build up as much as I can right now."
Information from The Associated Press was used in this report.