The striker was set to feature for the reserves in their final game of the season against Fulham last night.
But he pulled out minutes before kick-off after suffering pain in his groin during the pre-match warm-up.
There is better news regarding David James, who is recovering well from his calf problem and is now taking part in outside work.
The England keeper was today undergoing another scan to assess how his calf problem is responding.
But he is pushing for a recall against Fulham.
Nugent's absence has sparked fears he may have aggravated the injury which required an operation back in January, at the time ruling him out of action for two months.
In his absence last night, Paul Groves' side grabbed a last-gasp 1-0 victory through Danijel Subotic.
Pompey now face an anxious wait to discover the full extent of Nugent's problem with the FA Cup final looming.
Meanwhile, there's better news on the injury front for the rest of the Blues' walking wounded.
Sulley Muntari and John Utaka were yesterday back in training having missed the weekend Middlesbrough defeat.
Pedro Mendes is set to resume training by the end of this week following a hip problem.
Meanwhile, long-term casualty Noe Pamarot last night made his return for the reserves following three months out with knee ligament damage.
Harry Redknapp has already indicated he will put a full-strength side out for Sunday's Fulham fixture, with all the former casualties now in the frame.

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