The on-loan Crawley defender suffered a hip injury during last weekend's 1-1 draw against Carlisle and will be missing for around a fortnight.
Former Charlton full-back Yassin Moutaouakil is poised to come in for Cooper in what is likely to be the only change to caretaker boss Guy Whittingham's starting line-up.
But veteran striker David Connolly could be added to the bench after three weeks on the sidelines.
The Irishman has missed the last four matches with a hamstring problem but has this week returned to training.
Pompey have slumped to the bottom of the table despite successive draws and are still without a win since October 20.
