Head Coach Pete Carroll announced the fourth-year receiver will go on the shelf after tearing a labrum while diving for a pass during an Aug. 13 practice.
The need for surgery was confirmed by tests Monday.
Carroll had planned to alternate Carlson with Zach Miller, who signed with Seattle this month.
"We were really counting on this," the coach said. "We were so excited about having Zach and John play together. Unfortunately, that's not going to happen now."
Carlson has played in 47 games career games, totaling 137 catches for 1,519 yards and 13 touchdowns.
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