No decision has been made about surgery. "The doctor feels as though it's significant," Padres manager Bud Black said.
Marquis, 34, allowed six runs on eight hits with three walks over 5 1/3 innings in a loss to the St. Louis Cardinals in his last start on Friday.
Marquis was 9-5 with a 4.05 ERA in 20 starts this season, but went 0-3 with a 5.13 ERA over his last six starts.
"You look at the win-loss record and the overall ERA, though it has been climbing as of late, and we won a lot of games he started," Black said.Marquis signed a deal with the Padres last season after being released by the Minnesota Twins in May and then re-signed with San Diego on a one-year, $3 million deal in the offseason.