Joko Raharjo, one of Suharto's doctor at Pertamina hospital, said on Tuesday that the sepsis had destabilised his heart, which could prove fatal.
The latest development comes a day after doctors said one of Suharto's lungs had pneumonia, one of the gravest threats to patients with multiple organ failure.
Earlier on Tuesday, they said Suharto's heart had showed signs of improvement but warned that his condition was still unstable and could become worse.
Aides said privately that the former five-star general had appeared to be on the verge of death several times.
|Mahathir was among a string of regional leaders|
to visit Suharto in hospital [EPA]
Marjo Subiandono, who heads the medical team at the Jakarta hospital, said Suharto was responding to simple requests, taking hold of a hand when he was asked to.
"We are quite amazed at how strong he is ... maybe because he is a former soldier, a general," he said.
Several regional leaders have been visiting Suharto since the weekend, including Mahathir Mohamad, Malaysia's former prime minister, Hassanal Bolkiah, Brunei's leader, and Lee Kuan Yew, Singapore's former prime minister.
"[I am] very sad, because when I last met him he could still think clearly," Mahathir told MetroTV after visiting Suharto on Monday.
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.