The San Siro side currently sit in eighth place in Serie A following Sunday's 1-1 draw with Sampdoria, with their hopes of European qualification fading fast.
Boban believes his old side are scarcely a team and says that Inzaghi's tactics are "anarchy".
"The problem is that the Milan have very scarce players," he said to Sky.
"It's almost impossible to create a team with these players. I don't understand what they offer.
"Also Inzaghi does not have a great gameplan. But it's hard to get them to run together. There's a bit of anarchy. It's very tough.
"I have realised the value of the Milan squad. It's very difficult to be satisfied after a game like that."
Milan's next game is a derby clash with Inter on Sunday.