Hughes is keen on signing the Paraguay international in the January transfer window.
“We have made an improved bid, a substantial bid, and it was rejected,” said Hughes.
“We still want to bring Roque Santa Cruz to the club if we can, but he’s still Blackburn’s player and at the moment they don’t want to deal at the level we are at.
“We will make any future decisions in regards to their response.
“We bid £12million in the summer and it (the latest offer) was significantly higher than that.
“We will now have to wait and see.”