Hughes was responding to a report in the Daily Mail newspaper that the Burundi-born 23-year-old had tested positive out of competition in September for a recreational drug.
"There was an FA disciplinary matter and Saido had an eight-week suspension, I believe," he said.
"We were aware of that before we signed him. In terms of more detail you would probably need to refer back to his former club.
"We aren't in a position to give any more details as we don't have them. He had issues at his previous club for 18 months, which this is obviously a part of."
The FA does not comment on its social drugs policy regulations and a spokesman had nothing to add.
West Brom host Stoke in the Premier League on Saturday and Hughes said there was no reason why Berahino would not play against his old club.
Tony Pulis, the former Stoke manager who is now in charge at the Hawthorns, also confirmed the player had served a suspension.
"Saido served a ban while he was here but I won't comment why. He didn't play for me because he wasn't fit enough," Pulis said.
"Saido is no longer an Albion player. It's one for Stoke to handle."
(Reporting by Alan Baldwin, editing by Ed Osmond)
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