The bid he has put in is reportedly around the £16 million mark but Rovers are sitting tight at the moment.
"We have made an improved bid, a substantial bid for Roque Santa Cruz but it was rejected," said Hughes.
"We made a bid in the region of £12m in the summer and it (the new bid) is significantly higher than that.
"But we still want to bring him to the club if we can but he is Blackburn's player and they don't want to deal at the level we have made a bid at. That is their prerogative."