"Xherdan is still a little bit slow at the moment," Hughes said on the club's website.
"We've tried something a little different with him this week just to push him on but he won't be available for the weekend."
Johnson, who was sidelined for nearly seven months with a knee injury, could return to the side after recovering from a thigh problem he suffered in pre-season. The former Liverpool defender last played for Stoke in February.
"Glen joined in with the first team today (Thursday), which is good, so we fully anticipate that he should be okay now," Hughes added.
"We'll get some more training into him, certainly next week, we have league and cup games coming up so that's a good opportunity to get him and other guys up to speed."
Stoke, who are searching for their first league win of the season, are bottom of the Premier League on goal difference with just one point from three games.
(Reporting by Nivedita Shankar in Bengaluru; Editing by Toby Davis)
