The Cameroon international is struggling to find the back of the net in his first season in Italy and has criticised the tactics of coach Jose Mourinho in Europe.
But Moratti says: "Mourinho is going for a type of game that Eto'o must get used to and he must have a little patience.
"Samuel is still adjusting to a new league. As soon as he starts scoring goals, we will have no more doubts. Mourinho a great professional, can make mistakes, but I have no fear that he might do things professionally wrong."