Samardzija left a minor league outing on Wednesday after allowing two home runs and a double in a rocky fourth inning.
"To be honest, we are getting Samardzija looked at, his shoulder is getting looked at," manager Bruce Bochy said. "He had an MRI, can't give you anything until maybe after the game, until the doc looks at it and evaluates it and talks to Shark."
Samardzija, who was expected to the Giants' No. 3 starter after Madison Bumgarner and Johnny Cueto, had a 10.64 ERA in four Cactus League starts. His fastball velocity has been around 89-90 rather than his normal 93-94, Bochy said.
Lefthander Derek Holland, a non-roster invitee to camp, is the most likely candidate to replace Samardzija in the rotation to begin the season.