Mazzarri was replaced by Roberto Mancini last month.
"He is undoubtedly an excellent, quality Coach, and what's going on with Napoli now is the proof of that," said Moratti.
"In certain cases the Coach can't fit in properly with a club. Besides, many things have happened, such as the new ownership.
"This must have caused him problems, and the situation cannot have been easy.
"And it's understandable that an excellent Coach may not always perform the way he's expected to. It happened to me a few times with Inter."