Dom Thomas will undergo surgery after the Dunfermline winger was diagnosed with a tear to the meniscus cartilage in his knee.
The 25-year-old visited a specialist on Monday and has been advised to go under the knife to ‘tidy up’ the damage.
The Fife outfit are keen to book their talisman in for an operation this week as they seek to minimise the length of his layoff.
While Hughes was reluctant to put an exact timeframe on Thomas’ absence before the surgery, he will be missing for several weeks.
“Dom has a tear in his meniscus [knee] and, to be fair to him, has been playing through that,” explained Hughes. “It has flared up and started to be a problem.
“We had it scanned the other day and the doctor agrees with what showed up in the scan.
“He will go when for a tidy-up [operation] ASAP — hopefully within the next couple of days.
“It would be unfair to put an exact timeframe on it right now, but he was missed on Saturday and I think you could see that.”
Hughes, meanwhile, confirmed that Iain Wilson missed out against Hamilton due to an ongoing heel complaint while Reece Cole is suffering the effects of a dead leg.
It is hoped Rhys Breen will be fit to face Queen of the South on Saturday.
Graham Dorrans appeal to be heard on Wednesday
The Pars gaffer is similarly optimistic regarding the potential availability of Graham Dorrans.
The East End Park captain was dismissed against Accies after referee David Munro adjudged that he blocked a Marley Redfern shot with his arm.
While nothing can be done about the defeat, Hughes is counting on the decision being rescinded — with the Scottish FA’s fast-track disciplinary panel set to make their decision on Wednesday.
“Everyone can see that it’s not handball so we are hopeful,” said Hughes. “There is good video footage so we have our fingers crossed.
“It is part-and-parcel of football. We have all been there, we have all made mistakes.
“The Hamilton players were all claiming for it and his linesman could have helped him out a bit.
“But if the referee says that it’s handball, then he obviously hasn’t seen it.”