The latest setback is somewhat surprising because Bedard said he "felt fine" after throwing a bullpen session on Tuesday night at Kauffman Stadium.
Now, he will have dye injected into his shoulder on Friday and will not be able to throw for at least four days. It is uncertain whether he will make another start this season.
"You have to understand from his standpoint that he's very frustrated," Wakamatsu said. "He has had ongoing issues for two years now. I don't think [the discomfort] is as bad as before, but I think he feels that if he continues to pitch, we're going down the same path and would have to put him back on the DL."
He went on the disabled list for the first time this season on June 17 -- retroactive to June 9 -- with left shoulder inflammation and missed 25 games. He returned to the rotation on July 7 and made four starts before being placed back on the DL.
The Mariners split the four games Bedard pitched, but he worked into the fifth inning only once and regularly had high pitch counts.
"I know he wants to be out there pitching," Wakamatsu said. "Right now, we're trying to get some clarity."
Results from the MRI Bedard has on Friday will be compared to the one he had more than a month ago. That one showed that there was nothing structurally wrong with the shoulder. Rest and anti-inflammatory medication was the plan of attack.
If the next MRI also comes out clean and Bedard can resume his current recovery program, his return to the Seattle rotation would be delayed by at least one rehab stint in the Minor Leagues.
Until Wednesday, the Mariners were hopeful that Bedard could throw another bullpen on Friday and build his arm back up during workouts with the team, instead of going on a rehab assignment.
Furthermore, the Minor League seasons end in about three weeks, which limits the places Bedard could go for the rehab.
As it is, the immediate game plan goes no further than the MRI.
Wakamatsu said he was surprised by the latest setback.
"I thought we had a handle on it, but only [Bedard] knows his shoulder and what's going on in there," Wakamatsu said. "I had something similar when I played, so I have empathy for him. The MRIs taken on my elbow didn't show anything and it wasn't until I had it scoped that they found a tear.
"He wants to be pitching and we want him out there and there has to be something bothering him. The thing we're trying to do is find out what it is."
Bedard has a 5-3 record and 2.82 ERA in 15 starts this season. He was 6-4 with a 3.67 ERA in 15 starts last season.