The Uruguayan striker has been called up by his country despite only recently returning from injury.
Stuani has not played for Boro since September when he reported back from international duty with groin and hamstring problems.
Now back in full training, he missed the weekend’s loss to Hull City as the club did not think he was fit, but Uruguay have requested his presence and Stuani has made the decision to link-up with his country.
“Of course I can appreciate Karanka’s point of view and that of "El Maestro" [Uruguay coach Oscar Tabarez]. It's hard when you want to please everybody,”he said, in quotes covered by the Gazette.
But Karanka is not happy and told the club’s official website: “It’s difficult for me to understand because I think the national team is a result of the work you do for your club.
“So for this reason it’s difficult to understand how a player who has been injured for over a month is in the team.
“I didn’t want to take a risk with him. The players who are not training with me are not in my mind to take a position in the team so I don’t understand a team who selects a player that hasn’t been playing.
“But it’s not my concern. My concern is the players who are here, the players who were playing last month and those who are going to play in the next game.
“I can’t do anything as a coach and the club can’t do anything."
Uruguay’s team doctor Alberto Pan insisted that it was up to them to decide on whether a player was fit or not, as per FIFA rules which state a player must link-up with a squad – even if injured in order for him to be assessed by their medical staff.
Boro will now be hoping that Stuani is returned to them in full health and ready to play some part in a meeting with Queens Park Rangers on November 20.