The Zimbabwe international pulled a muscle in training, leaving City desperately short of attacking options with the 2008/09 campaign drawing ever closer.
"Unfortunately he picked it up a couple of days ago, he pulled a thigh muscle quite badly and the medical staff reckon he won't be available until into the new season," Hughes told the club's official website.
"Benjani ended last season quite well, and it is a shame but these things happen. You will always pick up injuries in pre-season, you hope that they will be slight ones that players can get over, but unfortunately this is a little bit more than that.
"We were quite strong, bodies-wise, we had quite a number of forward-thinking players but it could be that as we progress over the next couple of weeks we will be shorter than we thought we were going to be. We will have to have a look at it, we talk about how the balance of the squad needs to be right so we will make sure we will have enough strength there. It's a blow, and it was not something we were anticipating."