The Irish defender has yet to feature this season due to a groin problem and misses Friday's derby against former club Charlton.
"It's looking like Paddy will be missing for a longer period of time, at least another four or five weeks," Eagles manager Dougie Freedman told the South London Press.
"The injection he had has either given him an infection or been in the wrong area and it has swollen up again, making him very stiff and sore.
"As we speak he is four or five weeks away from it.
"It is a terrible bit of news for Paddy and we're just as disappointed. We've missed him and continue to miss him."