Martins Indi underwent a scan, and Hughes confirmed his player's prognosis ahead of Saturday's Premier League meeting with Tottenham Hotspur.
"Bruno, as we feared unfortunately, is likely to be out for quite some time," Hughes is quoted by Sky Sports News as saying at his pre-match press conference.
"He has really damaged the groin area, and to be fair we sensed that on the day because he was in a significant amount of pain. He has started his treatment already, but it will be a long process."
Martins Indi has made 11 appearances in all competitions for Stoke this season.