Deaths from the H5N1 virus have been steadily rising in archipelagic Indonesia where the virus is now endemic across 31 of its 33 provinces. The latest casualty was the second this month.
"Both tests are positive," Daswir Nurdin, from the ministry's bird flu information centre, told AFP.
Two tests for the H5N1 virus must be returned positive before someone is confirmed as dying of avian flu here.
Nurdin said that the latest victim died Tuesday in Pekanbaru shortly after arriving at its main hospital. He had fallen sick on October 31 and been admitted to a local hospital three days later.
"The number of cases (of bird flu in Indonesia) is 113, of which 91 have been fatal," he said.
Nurdin added that it was unclear whether the man had come into contact with poultry, the usual method of transmission of the disease to humans. Many Indonesians keep chickens or ducks in their backyards.
Azizman Daad from the state general hospital in the province told AFP that animal health teams from the Agriculture Ministry visited the area this week but didn't find any sick or dead chickens.
However, he said that an eight month baby living less than one kilometre away was suspected of bird flu and was now under treatment in the hospital, after the inspectors found bird nests.
"The blood samples of the birds have been sent to the laboratory and we are waiting for the result," he added.
Scientists fear that H5N1 will eventually mutate into a form that is much more easily transmissible between humans, triggering a global pandemic.
The original source is thought to have been wild migratory birds.
H5N1 has mainly affected Asia and some parts of Africa, but the Food and Agricultural Organisation warned last month that the virus could be transmitted to poultry in Europe by ducks and domestic geese seemingly in good health.
Besides Indonesia, deaths have been recorded in Azerbaijan, Cambodia, China, Egypt, Iraq, Laos, Nigeria, Thailand, Turkey and Vietnam.
The human outbreaks sparked a drive in recent years to bolster preparedness for a possible pandemic, including stockpiling of antiviral drug treatments, greater vaccine research and advance emergency planning.
There has been a resurgence in recent weeks in Vietnam, another of the countries worst hit by bird flu, with a sixth province reporting deaths in poultry on Thursday.
The communist nation had managed to control the situation with mass culls and vaccinations but it resurfaced in May and October.
Authorities in Indonesia, which reported its first human case in 2005, were initially criticised for being slow to act to curb the virus' spread.