The 26-year-old had an operation on a groin problem last season but that has now caused problems with the player's hip.
City manager Alex McLeish told the club's website: 'In all likelihood, the big 'un has got to go for an operation and we could be talking three to four months.'
Under the knife: O'Connor is facing a lengthy spell on the sidelines
'Garry's problem is related to what he had last year. He had an operation on part of the groin ligament in there because of wear and tear.
'I've not got the full technical details but the wear and tear has caused a little bit of bone growth or something has calcified, so he'll have to get shaved because it's affecting his mobility in that area.
'We think he's got to have an operation at some stage on his hip before he plays again. That is the kind of road we're going down, so it's another man down which isn't great in terms of our striking options.'
With Marcus Bent on loan at Middlesbrough, the injury leaves McLeish with just Cameron Jerome, Christian Benitez and Kevin Philips as senior strikers in his squad.
McLeish may now have to go into the transfer market in January to replace O'Connor, who has one goal to his name this term.
'He's basically someone who gives us a wee bit of a presence and otherwise we lack that,' said the Scot. 'Cameron is the outstanding candidate in that respect after O'Connor.
'Of course we've got (James) McFadden who can play through the middle, but we've got Benty out on loan at the moment, so I need to wrap these lads in cotton wool.
'I'm not too unhappy with the way the strikers are playing but we just don't want anything to happen to them.
'They're playing very well and I'm pleased with their form but it's important we keep them fit and also keep Kevin fit.'
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