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 is fully conscious. He can follow instructions and answer our questions in a weak voice"
Jusuf Misbach, Suharto's doctor
"He scratched himself and raised his hands. It's an amazing accomplishment," he said.
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.
Suharto ruled Indonesia for 32 years, but was forced to step down in 1998, amid widespread protests triggered by the Asian financial crisis.
Since being toppled , he lived a reclusive life in a comfortable villa in downtown Jakarta.