Murphy, on a season's loan at PNE from this weekend's FA Cup opponents Cardiff City, hasn't played since the middle of October after tearing an ankle ligament in training.
He was in the latter stages of his recovery from that but has now suffered a calf injury.
Lowe referenced Murphy's injury during a press conference on Wednesday afternoon ahead of Sunday's visit to Cardiff.
It is otherwise quite a clean bill of health ahead of the weekend, Connor Wickham still sidelined although he has been back in training recently after hamstring surgery in the autumn.
Lowe said: "Josh Murphy and Connor Wickham won't be available The rest are all in contention, they have all trained today.
"There was a recovery group from the game and a top-up group which involved all the lads who have been injured.
"Connor is in a situation where he has trained a few days and then been out a few days
"There is nothing major with him but his contract runs out in 10 days.
"Josh Murphy has had a bit of a setback with a calf injury. We don't know the timescale just yet but he's definitely had a setback.
"We will review that over the next few days but he certainly won't be available for the next few weeks.
"Other than that, everyone will be available for selection,"
Lowe said he would be having talks with Wickham soon.
The striker signed a short-term contract in September after being on trial for a month but badly damaged a hamstring in his second appearance.
Lowe said: "I need to sit down with the player first and foremost and take it from there. Over the next few days you might hear about it.
"We obviously have a duty of care to the player and we'll sit down and have a good chat."
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