The 25-year-old's transfer is likely to be announced later on Friday, but Hughes doesn't expect it to be wrapped up in time for the Dutchman to be available for Stoke's opening match of the season against Everton on Saturday.
"The deal needs to be done before midday for him to play tomorrow but that's not likely to be the case," said the Potters boss.
Martins Indi did not miss a Premier League match after joining on a season-long loan deal from Porto in August last season, making 35 league appearances in total.
Hughes is hoping more players will arrive at the bet365 Stadium before the transfer window shuts in 20 days.
"We are still looking to bring in more players to freshen up the squad," he added.
"I'm aware we've lost a bit of experience in the dressing room but we've still got good players here who can step up to leadership roles."