Doctors also said that pneumonia had spread to both his lungs, causing a fluid build-up.
"There are new infections in several parts of his body," said Marjo Subiandono, a member of Suharto's medical team.
"The increased sepsis is threatening his life."
Joko Raharjo, the chief doctor, said warned that Suharto's age and weak immune system were working against him.
"We are trying hard to find and detect the bacteria and treat him with proper antibiotics, but we cannot guarantee it will be successful."
Last weekend doctors were optimistic about Suharto's condition, saying he was staging an "amazing recovery" and had spoken, eaten and responded to simple instructions to move his hands.
The former army general's condition has been fluctuating since he was hospitalised early this month.
He has suffered multiple organ failure, breathes with the help of a ventilator, is hooked to a dialysis machine and is being fed through a tube.
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.