Baek experienced soreness in his elbow on Saturday in what was expected to be his last Minor League appearance before joining the Padres' starting rotation. He will fly Sunday from Portland to San Diego and will be examined by team physicians on Monday at Scripps.
Baek yielded five earned runs on six hits in 3 2/3 innings against Salt Lake, the Angels' Triple-A affiliate at PFE Park in Portland. He struck out six batters with no walks.
"He left the game around 70 pitches when his elbow became painful. It's a blow to us and a blow to Cha Seung," San Diego manager Bud Black said. "This is a situation we didn't expect. That's a setback."
Baek, who was expected to be the No. 3 pitcher in the starting rotation, suffered an injury to his right forearm in the last week of Spring Training and was placed on the disabled list. He had made two appearances with Class A Lake Elsinore.
Black said the soreness Baek reported Saturday was in a different spot on the elbow.
Though no move had been announced, it was expected that Baek would rejoin the team this week and would possibly make a start Friday when the Padres return to San Diego for a three-game series against the Reds.
Now his return is in doubt. Black said he will know the results of the tests that will be performed by the Padres' physicians sometime this week.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.