Walker, the No. 6 rated prospect in baseball by MLB.com, was a consideration to return from his own shoulder issues by Sunday, but he had his own rehab start with Triple-A Tacoma wiped out Tuesday when his shoulder felt tight before he even began throwing.
General manager Jack Zduriencik said Walker had an MRI on Wednesday in Seattle that showed the impingement.
"We're going to back him off for two weeks and treat it and eventually work him back to the mound and start the progression again," Zduriencik said.
Walker was slowed at the start of spring by shoulder soreness and was shut down completely for a week in early March before working his way back through a pair of Minor League rehab starts.
"I think it is the same general area," Zduriencik said. "He just wasn't comfortable. So we sent him for tests and now we'll back him off and treat it and see where we're at."
The Mariners have been hit with a series of pitching issues, with Danny Hultzen, another premier prospect, already lost for the year following rotator cuff surgery and All-Star right-hander Hisashi Iwakuma still a couple of weeks from returning from a sprained tendon in his finger.
"It's amazing," Zduriencik said. "Everybody in baseball seems to be going through the same type of things, but ours is a little more severe than most. Nevertheless, this will give others an opportunity."
Among the current Tacoma pitchers, left-hander Anthony Fernandez, 23, is the one healthy starter who is on the Mariners' 40-man roster. Brandon Maurer is another possibility and he has Major League experience, but Maurer is just returning from back problems and hasn't pitched more than 3 1/3 innings this season.
Beavan also is going to be out at least two weeks, which is a frustrating situation for the 25-year-old right-hander after he'd just been recalled after Paxton strained his left oblique muscle in his third start of the year.
Beavan said he essentially has "dead arm" from a knot in his shoulder that isn't allowing him to throw freely.
"I just had no life on my ball," he said. "It's just frustrating because I had a great opportunity to help these guys and fill the void of other guys being down. Now I'm in the same situation, but hopefully it's something where in the next 10 days we can get out of there and slide back into the action and help us win some ballgames."
Beavan is flying back to Seattle on Thursday to begin rehab treatment with trainers in Seattle.