Owens, who has featured on three occasions for the Scarlets this season - against Glocuester, Ulster and Leinster - suffered a neck injury in training at Parc y Scarlets last week ahead of the Guinness PRO12 third round home clash against Benetton Treviso.
Scarlets Head Coach Wayne Pivac said: "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.
"Ken had been playing well but the focus now is to get see him through the surgery and get him back here with us for rehabilitation. We're very pleased to have Emz (Emyr Phillips) step straight in there and play like that (against Benetton Treviso)."
Scarlets Head of Performance Andrew Walker said: "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 undergo surgery early next week after which he will return to the region for rehabilitation. He will be sidelined for a period of up to 12 weeks.
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