The World Health Organisation said the Indonesian was in intensive care and that "initial investigations suggest sick poultry as the possible source of infection".
The deadly virus has claimed 58 lives in Indonesia, more than in any other country.
"The challenge was to identify where the virus was hiding and how it was circulating"
Henk Bekedam, WHO representative in China
Chinese officials said a 37 year-old farmer from the eastern province of Anhui had contracted bird flu in December but was released from hospital after he "fully recovered".
China's health ministry and the Centre for Disease Control and Prevention confirmed on Monday that the farmer surnamed Li had tested positive for the H5N1 strain.
Those who have had close contact with him were quarantined for medical observation but were released after showing no signs of illness.
Medical officials were baffled as to how Li had contracted bird flu when there had been no reported outbreak among poultry in the area.
China has the world's biggest poultry population and millions of backyard birds roaming free.
Henk Bekedam, WHO's China representative, said the challenge was to identify where the virus was hiding and how it was circulating.
"It's not to say that the virus is not somehow still circulating, but that the detection of that circulating virus has become much more difficult because of the active engagement of the government in avian influenza control," he said.
Scientists fear the virus could mutate into a form that can be passed on easily between people, leading to a pandemic.
The last reported human case of bird flu in China was in July last year when a farmer died in the northwestern region in Xinjiang.
In Vietnam, tests on 70 dead ducks were positive for the H5N1 virus, a government report said on Wednesday.
Discovery of the dead birds prompted health workers to slaughter 1,800 more ducks in two communes in Kien Giang province in the southern Mekong Delta, the animal health department said.
Checkpoints have been set up in the two areas to prevent movements of birds for sale.
The WHO said bird flu has killed 42 of 93 people infected in Vietnam.
The virus still mostly affects bird but it has infected 263 people in 10 countries since 2003, killing 157 of them.