The 24-year-old fell awkwardly during the 2-1 victory over Bolton on Tuesday having notched his 15th goal of the season in all competitions, and subsequent scans have confirmed Rangers' fears.
Dr Peter Florida, the Rs' head of medical services, told the club's official website: "Charlie went for a scan on Wednesday afternoon and unfortunately it has shown he has suffered an injury to his shoulder.
"He's done some damage to the bone and cartilage in the joint, as well as the soft tissues around it, and will need an operation to correct the problem.
"We'll start his rehabilitation immediately but he's likely to be sidelined for a prolonged period."
Austin added: "I'm obviously desperately disappointed. Injuries are part and parcel of football but I was really enjoying my football so it's a bitter blow.
"I'll work tirelessly in my rehabilitation to make sure I return as quickly as possible and in the meantime, support the lads as we continue to push for promotion."
QPR currently sit in second place in the Sky Bet Championship with third placed Burnley snapping at their heels just three points behind.