The 36-year-old right-hander told reporters after yielding nine runs on over just 2 1/3 innings Sunday against Miami he has been battling shoulder soreness since April 24.
He handled the Pirates on one hit over six innings on that day, but has since been tagged for 17 runs over six frames in two starts.
The two-time Cy Young Award-winner's ERA has ballooned to 8.65.
"I just got up after that start against Pittsburgh [on April 24] and had soreness in there and wasn't able to get rid of it," Halladay said.
"Until we do any diagnostic work, we won't know exactly what's going on with him, but clearly it doesn't seem like he's very healthy," the GM said.