Manager Terry Francona said the club and its medical staff looked at pictures from his MRIs taken on Wednesday.
"He's really tender," said Francona.
Ellsbury was activated from the disabled list last Saturday in Philadelphia after suffering a hairline fracture on four ribs on his left side during a collision with third baseman Adrian Beltre on April 11 at Kansas City.
Ellsbury missed his third consecutive game Thursday night.
"We've got to get to the bottom of this. We're not at the bottom of it," said Francona. "We don't want to rush into putting him on the DL and at the same time he's not ready to play because the way he feels. We'll get to the bottom of it, but we're not there yet. Whether we have to get more opinions, we'll do whatever we think is necessary."
Dr. Thomas Gill spoke with Francona and Ellsbury prior to the game.
"We're trying to figure out the best way to go through this," Francona said after Boston's 4-3 loss to the Royals. "He'll have one more examination and hopefully we'll have some more insight on what's the best way to go with this."
After Wednesday's game at Tampa, Ellsbury said, "[The pain] is along the same ribs that cracked. All the ribs are moving, so it can affect the back ribs as well, where it hits the front of the spine. So you not only feel the impact at the direct place where you were hit, but the back side, too, along the band. I felt that originally, but I hadn't felt it again until now.
"You look at the point where we got the break, but sometimes people forget to look at other places,'' he added.
Ellsbury remains irked that the injury was originally described as bruised ribs. "I think they downplay it because they misdiagnosed it,'' he said Wednesday. "They said you treat it all the same way. Remember that comment? How do you treat a bruise the same as a break?''
Gill had responded to that question directly when further tests showed the hairline fractures.
"It pretty much is our standard or anyone's standard that you do a careful physical examination, you get your X-rays, and then assuming the X-rays don't show any obvious fractures or lung injuries or any soft tissue injuries, that's pretty much the standard of care for looking at potential rib or chest injuries,'' Gill had said.
Joe McDonald covers the Red Sox and Bruins for ESPNBoston.com. Gordon Edes of ESPNBoston.com contributed to this report.