Hughes is worried that the 24-year-old Portugal-born Dutch international may have fractured his cheekbone.
"The fear is that it may be a crack in a cheekbone," Hughes told BBC Stoke.
"He's got a big bang on the side of his cheek. We'll have to wait and see as the swelling comes down."
Martins Indi, who is on loan from FC Porto until the end of the season, has been a regular this season but has told BBC Stoke that he has a number of issues to make a decision on whether he will still be at the club next season.
Stoke are already waiting on the results of an MRI scan for England keeper Jack Butland, who pulled out of his planned return following a broken ankle in Friday's Under-23 game at Reading.
The Potters, up to ninth in the Premier League after a run of just one defeat in eight matches, are already short of defensive cover.
Phil Bardsley is unlikely to be available before Christmas after visiting a London specialist about his knee injury - a blow softened by Glen Johnson's return to action.
But Geoff Cameron has missed five matches with a knee injury and illness, while skipper Ryan Shawcross sat out Saturday's game with a calf problem.
Meanwhile, striker Ibrahim Afellay is back in training after suffering a knee injury in April but, as expected, he did not play on Friday at the Madejski Stadium.
Stoke City loan defender Bruno Martins Indi has become the latest concern for manager Mark Hughes after suffering a head injury in Saturday's 2-0 home victory against Burnley.