The transfer is yet to be formally announced by the club, but both the New England Revolution striker and Hughes have now claimed that the move will go ahead.
However, complications regarding the 21-year-old's work permit mean he would need to be sent out on loan upon his arrival at the Britannia Stadium.
"We have tied Juan Agudelo to the club, but we aren't in a position where we can play him because of the unbelievable situation with the work permit," Hughes said.
"We didn't want to lose him because we feel he is arguably the biggest talent in America.
"We have taken him, and we now need to get him abroad somewhere until the end of the season to play some games and then reapply for the work permit in the future.
"Without going into the specifics of the deal we are determined to get him in here, but if we do hit a brick wall we may have to hold our hands up and say there is nothing else we can do. We are exploring every option available to us."
Agudelo would become Stoke's third signing of the window, having made Stephen Ireland's loan from Aston Villa permanent and taken Manchester City's John Guidetti on loan.
"John Guidetti gives us a different option up top which is good," Hughes continued. "He is a player who can play up front on his own.
"He has fantastic intelligence around the box, and when he gets opportunities he usually scores. He will go straight into the squad for the game at Crystal Palace."
Following reports of a falling out between Hughes and forward Kenwyne Jones, the Welshman confirmed the Trinidadian would not be involved against Palace.
"I was disappointed with what happened with Kenwyne last weekend," he added. "We spoke on Monday, just to get an understanding of why it happened.
"He has been in this week training, but he won't be a part of the squad this weekend.
"We have had no contact from anybody for him this window, so maybe the information he is getting isn't correct.
"We're not looking to get rid of any striker. If we do, it will be on our terms rather than anyone else's."
