Sixty percent of those died of Newcastle disease and 40% of a combination of Newcastle disease and avian influenza, said director general of animal husbandry, Sufjan Sudardjat on Sunday.
He said the avian influenza disease had hit almost all parts of the country.
Officials said there was no evidence so far the disease had spread to humans.
Indonesia had previously blamed the deaths of thousands of chickens on Newcastle disease, a virus that is harmless to humans and does not affect the safety of poultry meat.
Millions of chickens are being slaughtered across Asia after an outbreak of the highly-infectious avian flu strain which has killed six people in Vietnam.
Indonesia earlier confirmed an outbreak of avian influenza among chickens, but has no evidence so far that the disease has spread to humans, a senior official of the agriculture ministry said on Sunday.
"It's been confirmed avian influenza exists, but no human cases so far," animal health director Tri Satya Putri Naipospos told reporters.
Indonesia had previously insisted it was free of the influenza and blamed the deaths of thousands of chickens on parts of East Java and the tourist centre of Bali in the past three months on Newcastle disease.