
Bodies had been recovered, including three people who were on the ground when the Hercules C-130 crashed in Magetan district while on a regular flight to the country's easternmost province of Papua from the capital, Jakarta, officials said.
"I heard two explosions, and the plane burst into flames," a resident identified only as Tofa told Metro TV.
The commander of the East Java Madiun Iswahyudi Air Force base, Marshal Bambang Samudra said a total of 105 victims had been evacuated, 90 of them were dead, 10 sustained serious injuries and five others suffered minor injuries.
Samudra revised upward the number of people on board the plane, saying the aircraft was carrying 110 people when it crashed at about 6:20 am (2320 GMT Tuesday) about 7 kilometres west of the East Java city of Madiun.
He said efforts were underway to evacuate several other people who remained trapped.
The East Java military commander, Major General Suwarno, had said earlier that there were 112 people on board the plane, 98 passengers - including 10 children - and 14 crew.
A report from Madiun by Elshinta private radio put the death toll at 96 with more than a dozen others injured.
Television footage showed the plane split in two and black smoke billowing into the sky from its burning fuselage and partly intact tail section located in a rice field.
Witnesses said the plane was shaking and one of its wings was stripped away before it plummeted to the ground. Charred bodies were scattered in the surrounding rice paddy and nearby bushes.
A local official said some survivors suffered serious burns. "The victims are still being evacuated from the scene," Wardi, who like many Indonesians uses only one name, told Metro TV.
An official at Iswahyudi hospital said 19 victims were brought to the hospital. Nine other injured people, including two children, were sent to another hospital in the same town. Several of them were in critical condition.
"Several of them were suffering serious injuries, bleeding severely," said Sumringah, a nurse at Madiun's Dr Sudono hospital. "Some of them were unconscious when they arrived here in this hospital."
The plane was on a routine delivery flight to Papua with stopovers scheduled in Madiun, Makassar in South Sulawesi and Ambon in Maluku province, Bambang said.
It was the second fatal accident involving an Indonesian Air Force plane in recent weeks. On April 6, a Fokker F-27 crashed and burst into flames in West Java's capital, Bandung, killing all 24 officers on board.