Sterling came through the academy at QPR before being snapped up by Liverpool, where he is now starring.
Hughes said: "Massive changes in the academy will ensure we keep our best players. And it's a big thing to bring your own players through.
"Those players have a real empathy to the club and the fans have a real empathy with them.
"When you have a player of the talent of Raheem Sterling and you can't keep him - there's something wrong fundamentally."