A 24-year-old Indonesian man infected with bird flu died in the capital Jakarta, the health ministry said, in the country's third fatal case in three months.

"Test results from the man who died confirmed that he was infected with bird flu," health ministry head of communicable diseases Tjandra Yoga Aditama told AFP.

The man likely contracted the H5N1 avian influenza virus from birds living around his house, Aditama said.

"We have taken samples from birds around his home and are waiting for lab results to determine if they were infected with the virus," he said.

The Jakarta Post reported that the man died Saturday after being rejected by a hospital specialising in bird flu, and had on New Year's Eve been misdiagnosed by two other hospitals with a gastric infection and dengue fever.

The man died on on his way to another hospital on the capital's northeastern outskirts, reports said.

The report quoted neighbours as saying the man's family kept pet pigeons in their home.

Indonesia has been the hardest-hit by bird flu, with 150 deaths reported between 2003 and 2011, according to the World Health Organisation

Nine Indonesians died from the virus last year, including two children on the resort island of Bali in October.

Vietnam culled more than 2,500 chickens this week on bird flu fears after several animals were found dead on a farm in the Mekong Delta, and China reported its first human fatality from the disease in 18 months late December.

The virus typically spreads from birds to humans through direct contact, but experts fear it could mutate into a form easily transmissible between humans, with the potential to kill millions in a pandemic.