Beattie was an instrumental figure in the Warriors' charge to the inaugural Magners League Play-Offs last season, playing in 15 of his side's 19 Magners League fixtures.
He became a regular in the Scottish national XV alongside in an all-Glasgow back row that also featured Kelly Brown and John Barclay taking his total number of international caps to 14.
Beattie had been expected to be a key figure for both club and country once again this season, with Scotland looking to build on their Six Nations win in Ireland and their series triumph in Argentina and the Warriors keen to improve on last season's third-place finish in the Magners League.
Having been examined by orthopaedic surgeon Julie McBirnie at Spire Murrayfield Hospital, Beattie will have an operation at the same hospital in the next few days and is optimistic that he will still be able to play a significant role in Glasgow's season.
"It's probably too early to say definitively how long I'll be out," Beattie told the official Warriors website.
"Prior to the operation, the surgeon is talking about a six-month window to get back but that's quite cautious and if I regain the strength at the same level as my right shoulder then it should be sooner."
Beattie's absence will come as a major blow to the Warriors but it has already been compounded by the news that he isn't the only Glasgow flanker to require shoulder surgery.
Fellow Firhill favourite James Eddie is also set to go under the knife after suffering a dislocation in training last week.
The 25-year-old featured six times in the Magners League last season but had been earmarked to play a more significant role following the departure of Brown to Saracens.
However, Eddie will join Beattie in undergoing surgery this week, with no date yet set for his comeback.
"We wish both Johnnie and James a speedy recovery and we're grateful for the expert medical attention they are receiving," said Warriors head coach Sean Lineen.
"Currently there are a number of bumps and bruises within the camp. Happily, however, our physiotherapists are confident that the vast majority of players on the treatment bench at the moment will be fit for our first Magners League game against Leinster in September.
"On the back of last season's endeavours and three summer tours with national teams in which we had 20 players involved, a number of our players have taken a few knocks. It's unfortunate but it's an opportunity for the youngsters to shine over the next few weeks."
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