The 27-year-old will miss Wales's Autumn Internationals after suffering the injury during a scrum session in training earlier this month.
Scarlets head coach Wayne Pivac told the club's official website: "It's a shame for both Ken on a personal level and the team as a whole that he will require surgery on the injury he received earlier last week to his neck.
Head of performance Andrew Walker added: "Unfortunately Ken injured his neck in a training session a week last Tuesday. Following thorough investigations the scans have confirmed the he's injured a disc in his neck.
"After a thorough process, involving consultations with three neck specialists, we have decided that surgery is the best course of action."
Owens will go under the knife early next week.