Eaton experienced discomfort in the elbow Monday while playing for Triple-A Reno in Round Rock, Texas.
After serving as a designated hitter for most of the month and strengthening his arm, Eaton began playing in the outfield last Friday and Saturday for Class A Visalia. He made a couple of throws in games there and did not have any problems.
After a travel day Sunday, Eaton played in the outfield for Reno on Monday, and the problem in the elbow cropped up again.
"Everything was going really well," Eaton said. "Made a couple of strong throws in Visalia and then got to Round Rock, and the first one there, I felt a little discomfort. Then I felt it again, and I just knew this isn't right. Against my better judgment -- because I usually try to play through stuff like that -- I told the trainer, and they got me right out of the game."
Eaton underwent treatment on the elbow Tuesday, "and it didn't react well to it."
The elbow problems initially developed for Eaton in March, and he was shut down and placed on the disabled list.
Had this recent setback not occurred, it appeared Eaton would have been able to rejoin the D-backs before the end of the month.
"It just feels like someone punched me in the stomach," Eaton said. "It's tough to have a setback like this, but I have to try and learn what I can during this and go forward. Try to take as much good out of a bad situation."
Eaton remained optimistic heading into his appointment with Lee.
"It doesn't hurt any more or as bad as before," he said. "I think it might just be a couple-of-days shutdown, but I'm just speculating. I was really close, a couple of days away, from being fully built up, so if I only need to miss a couple of days, it shouldn't take me too long. We'll see."
Steve Gilbert is a reporter for MLB.com. Read his blog, Inside the D-backs, and follow him on Twitter @SteveGilbertMLB. This story was not subject to the approval of Major League Baseball or its clubs.