The 26-year-old went off injured in the Blues’ 3-0 win against Hereford two weeks ago – the striker initially thinking it was a minor knock.
But an MRI scan has since revealed that the summer signing had in fact torn his anterior cruciate ligament.
"I turned and just felt it pop and I knew that something wasn't right, but I was expecting it to be something minor," Hughes told Chesire Live.
"I went for an MRI and the results got sent back to the club and they told me it was really bad news and that I've torn my ACL.
“It looks like I'm going to need surgery and that means six months before I can even start thinking about kicking a ball again.
“I was in a bit of shock and it's so gutting as I've never had a serious injury and now I'm going to miss the rest of the season just when I was starting to play my best football.
“I felt I was absolutely flying so this has come at the worst possible time."