Walters' current contract with the club runs out at the end of the season and discussions over an extension have stalled, with the 32-year-old wanting a deal through to the summer of 2018 but Stoke only offering one to 2017.
Meanwhile, he has been in fine form this term, with his spectacular strike in Tuesday's Capital One Cup clash with Chelsea his fourth club goal of the campaign to add to two he has netted for the Republic of Ireland.
Stoke have consistently said they want to keep hold of Walters, who handed in a transfer request amid bids from Norwich being rejected towards the end of the last transfer window.
And asked on Thursday about the situation, Potters boss Hughes said: "There is (a danger of Walters leaving), but it is not what I want and is not what I feel Jon probably wants.
"There is scope to return to the table - I'd like to think so anyway.
"The issue is the length of contract - it is not about our feelings about Jon's ability
He is playing exceptionally well.
"I would like to think we can come to some decision positively not only for ourselves but for Jon himself, because I think he wants security and to be settled in his work.
"I'm hopeful we will get to a point where we can sit down again and find some common ground."
Hughes was speaking at his press conference to preview Saturday's Barclays Premier League trip to Newcastle.
Stoke go into the contest in high spirits having set up a quarter-final at home against Sheffield Wednesday with victory on penalties over Chelsea at the Britannia Stadium.
They have been left with some injury concerns as a result of Tuesday's game, but captain Ryan Shawcross - who made his maiden first-team appearance of the season having recovered from back surgery - is not among them.
Hughes said of the defender: "We checked on Ryan today and he looked fine - of all those who came through, he was probably the one in the best nick.
"It was a huge test for him given he has been out for a number of months
I don't think he anticipated he would have to go to 120 minutes in his first game back, but he came through it, and showed his qualities both in terms of his playing ability and his leadership that we have probably lacked on occasions.
"So it is a massive positive for us - he is fit and raring to go again."
Marc Muniesa limped off in that match and is set for a month out with a hamstring problem, while Geoff Cameron (thigh) remains sidelined, but their fellow defender Erik Pieters is available again after suspension.
Playmaker Bojan Krkic, rested for the cup tie, is also poised to return to action on Saturday.
Source : PA
Source: PA