The duo underwent knee ligament surgery earlier in the season, but the Welshman is hopeful both will return before the end of the current campaign.
The news will come as a boost to Walters, who has been missing since the win over Watford in March, and is still likely to need game time ahead of his potential selection for the Republic of Ireland at Euro 2016.
According to the Stoke Sentinel, Hughes told reporters: "He's [Walters] in and around the building, mainly in the treatment room, and so we are only passing in the canteen.
"But obviously I'm getting regular updates from the physios and the feeling is he will be available for games before the end of the season."
In contrast, an appearance at Euro 2016 looks unlikely for Johnson, who has not pulled on an England shirt since winning his 54th cap at the 2014 World Cup.
Nevertheless, a return before the end of the season will give the 31-year-old a glimmer of hope in forcing his way back into Roy Hodgson's plans.
Hughes added: "It's similar [the situation] with Glen Johnson if everything keeps progressing, so their seasons aren't over."
The Potters return to the Britannia Stadium on Monday night hoping to bounce back from a disappointing 4-1 defeat at Liverpool last week and put a dent in Tottenham Hotspur's Premier League title hopes.