Rafferty was Portsmouth’s first choice right-back at the beginning of the season, starting the opening seven games of the League One campaign.
However, injury has sidelined him since September and now the right-back’s problem has been aggravated and he is out for the long-term.
Cowley revealed that Rafferty will require another operation, on top of the one he has had already, and consequently he will be out of the mix for around three months.
The Portsmouth boss is understandably disappointed and feels it is a shock because Rafferty has prior to this season not had a bad injury record.
Speaking to The News, Cowley said: “We’ve had some disappointing news about Joe Rafferty, who has been confirmed will need an operation.
“He will have that on Monday and it’s really disappointing news.
“He’s had one operation and now needs another.
“We’ve had a scan, now the surgeon wants to go in and have a look.
“They’ll go in and take a much closer look in the operating theatre, then we will have more clarity.
“We are probably looking at three months.
“It’s the same groin, a slightly different joint, but it’s the same area, which is frustrating.
“It’s disappointment and frustration in equal measure, particularly for a boy who’s had very little injury background to this point, but they are the cards dealt to us, which we’ll have to accept.”
The current season is Rafferty’s first with Portsmouth and he will be hoping that he can put his injury troubles behind him when he comes back to the team and help them towards the latter end of the campaign.
