Speaking to reporters on Thursday Mardjo Soebiandono, the head of Suharto's medical team, said the former leader's condition remained unstable.
"Last night it was good, now it is not good," he said.
"A systemic infection means (the infection) is comprehensive, but we are still labouring to reduce this infection and from the available indicators, there seems to be some success."
Early this week Suharto, 86, surprised his medical team by surviving multiple organ failure but developed sepsis, a potentially fatal blood infection, soon after that.
Doctors said the infection has destabilised his heart and could lead to death.
They also found pneumonia in one of his lungs and were trying to prevent fluid from getting into his other lung.
He has since been placed on maximum drug dosage and remains under constant attention in intensive care.
In recent days regional leaders including Mahathir Mohamad, Malaysia's former prime minister, Hassanal Bolkiah, the Sultan of Brunei's, and Lee Kuan Yew, Singapore's former prime minister have all visited his bedside.
Suharto ruled Indonesia for more than three decades but was forced to step down in 1998 amid widespread protests triggered by the Asian financial crisis.
Critics say his rule was characterised by harsh repression of any dissent, and blame him for the deaths of hundreds of thousands of people.
The former leader, his family and close associates are also accused of siphoning off billions of dollars in government funds during his time in power.
But supporters say Suharto presided over a period of rapid development in Indonesia.
Suharto's fluctuating medical condition has sparked an ethical and religious debate in Indonesia over when and for how long artificial means should be used to keep a patient alive.
Doctors have no legal guidelines to go by, and instead are often guided by religious views or international practices.
A similar debate captured Indonesia's attention in 2004 when a man sought to legally end his wife's life after she had been in a "persistent vegetative state" for three months after a childbirth operation went wrong.
She regained consciousness before a ruling was issued.