Officials said some of the animals at the zoo in the city of Chilpancingo had been sold off, traded or eaten under Jose Ruben Nava’s orders.
Fernando Ruiz Gutierrez, the state environment department’s director of wildlife, said the four goats had been killed and cooked for an end-of-year banquet.
He added: “These four animals [were] slaughtered and cooked on the zoo’s premises, and were served as food at the year-end party.
"This put the health of the people who ate them at risk because these animals were not fit for human consumption."
Officials also said a zebra was traded for tools while a deer and Watusi cattle were sold to private buyers.
Mr Nava was replaced as director of the zoo on January 12 following the death of a deer.
It is not clear whether he has been formally charged.