On Monday night, Allen had to be withdrawn after a collision involving two Republic of Ireland players, and the midfielder was soon diagnosed with a concussion, which carries a mandatory absence from action.
Hughes has acknowledged that one of his key men will not feature against Manchester City on Saturday afternoon, and admitted that the former Liverpool man is still in the early stages of his recovery.
The 53-year-old told reporters: "Joe's not great. We've given him a couple of days to stay at home. He came in yesterday and felt a lot better, but in reality he's unlikely to be available.
"He had a bang to the head and found it difficult to remember the incident itself and that obviously tells you where he is in terms of the severity of it. So we have got to be careful and we are guided by the medical people here.
"It's a stepped return to full training and you've got to get through each step in the procedure to make sure you are 100 per cent ok to proceed to the next step."
Allen had started each of Stoke's seven Premier League fixtures before the international break.