Emre has not featured for The Magpies this season due to the problem, but has been named in Turkey's squad for Wednesday's friendly with Romania.
He is expected to play some part in the match and Allardyce is worried the former Internazionale schemer will come back with another injury.
The Newcastle boss accepts he cannot prevent Emre linking up with Turkey and is hoping Emre will not suffer a setback.
Allardyce: "Emre will probably go away with Turkey - there's nothing we can do about it. Emre hasn't played a game for us yet, so that's a worry.
"There's more chance of him getting injured than anyone else.
"He tells me that he'll only have half an hour or 45 minutes, so I hope that's the case and when he gets back, we'll get him up to speed."