The doctors said his breathing pattern was very quick and shallow and his blood pressure had dropped dramatically.
Siti Fadilah Supari, the health minister, told local radio that Suharto's heart had stopped beating, but he was successfully resuscitated.
""I was called again and told that the resuscitation had produced a response," she said.
"According to me, at an age like that, and if things are forced and no recovery can be reached ... it would be better to leave him in peace, to allow him to return to face God in peace."
Supari also said that the ventilator was not a guarantee that he would recover and it could cause him to suffer, so she was "rather shocked" when told he had been placed on the machine.
"The installation of a ventilator can result in false life," she said.
"Even though he is sick, Suharto must be held accountable for crimes he committed in the past"
Hasan, a protester outside the hospital
Family members of Suharto gathered at his bedside on Friday, witnesses said.
Hutomo Mandala Putra, Suharto's youngest son who also faces corruption charges and served time in prison for ordering the murder of a judge, was among them.
"On behalf of our family, we would like to thank fellow countrymen who have prayed for his recovery. For those who did so, hopefully you will receive something good in return," he said.
"The most important thing is that he gets better."
Former military leaders under Suharto including Prabowo Subianto, his former son-in-law, and Wiranto, a former military chief, also arrived at the hospital to see him as he lay behind a glass window, according to a family friend.
Last week, the retired five-star general was hospitalised with anaemia and low blood pressure, as well as problems with his heart, kidneys and lungs.
A series of strokes also left him with permanent brain damage and impaired speech.
Suharto has been in and out of hospital since he was forced to resign following intense public pressure at the height of calls for reform sparked by the 1997-1998 Asian financial crisis.
The sudden deterioration in his health condition had prompted calls for legal proceedings against him to be dropped but the government said this week it would press ahead with a civil case.
On Wednesday, a dozen student protesters gathered outside the hospital calling him to answer for his corrupt activities during his 30-year presidency.
"Even though he is sick, Suharto must be held accountable for crimes he committed in the past," a protester called Hasan said.
"Many people were killed when he rose to power. He used his influences to further his own interests and the interests of his family."
In recent days Suharto has been visited by Susilo Bambang Yudhoyono, Indonesia's current president, cabinet ministers, Muslim leaders and members of the ruling party.