The 27-year-old, who has 26 Wales caps, sustained the injury on Tuesday whilst training with the Welsh club side he captains.
"Following thorough investigations, the scans have confirmed the he's injured a disc in his neck," Scarlets head of performance Andrew Walker told their website.
"After a thorough process, involving consultations with three neck specialists, we have decided that surgery is the best course of action."
The Scarlets say Owens will undergo surgery next week and could be sidelined for three months whilst he recovers, meaning he will miss Wales's matches against Australia, Fiji, New Zealand and South Africa in November.
Owens made his debut for Wales at the 2011 World Cup and started in both of Warren Gatland side's summer tests against South Africa, scoring a try in their 31-30 second test defeat.
(Reporting by Sam Holden; editing by Justin Palmer)
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