Suharto developed a potentially fatal blood infection, as well as pneumonia.
Jusuf Misbach, Suharto's doctor, said he was still in intensive care, but was ready for early stages of physiotherapy.
"He is fully conscious. He can follow instructions and answer our questions in a weak voice," Misbach said.
"He scratched himself and raised his hands. It's an amazing accomplishment."
|"I believe Indonesians want him to recover and prayed for him" |
Murdiono, former Indonesian cabnet minister
Suharto was able to eat after his doctors moved a ventilator from his mouth to his neck on Saturday to reduce risk of bacterial infection.
Doctors said they were also successfully fighting his infection with antibiotics, and that his lungs and heart showed improvement.
"I believe Indonesians want him to recover and prayed for him," Murdiono, who served as a minister in Suharto's cabinet, said.
"It is a miracle. Thank God. He remains a hero and his services to this country deserve to be recognised."
Suharto ruled Indonesia for 32 years, but was forced to step down in 1998, amid widespread protests triggered by the Asian financial crisis.
Between 300,000 and 800,000 alleged communist sympathisers were killed during his rise to power between 1965 and 1968, in violence led by the Indonesian army and conservative religious groups.
Since being toppled, he has lived a reclusive life in a villa in downtown Jakarta.