Milito has been linked with a move to Madrid as part of coach Jose Mourinho's switch.
Mourinho is set to join Real Madrid this week after two seasons in charge of the Nerazzurri.
"I only say one thing, there's a difference between Milito and our coach, Mourinho," Moratti told the club's official website.
"Mourinho has a clause in his contract by which if the clause is exercised, he can leave.
"However, Milito doesn't and hence, the discussion is over."