Hariadi Wibisono, the Health Ministry's director of control of animal-borne diseases, citing the results of local tests said: "We found three positive bird flu cases in one family coming from Indramayu, West Java."
He said that was Indonesia's fifth cluster of bird flu cases, where people living in close proximity had fallen ill.
There was no evidence of human-to-human transmission and dead chickens had been found in the neighbourhood, he added.
The H5N1 virus is not yet known to pass easily between humans, but experts fear it could develop that ability and cause a global pandemic that might kill millions of people.
If confirmed by outside laboratories recognised by the World Health Organisation (WHO), the latest cases would take the total known deaths in Indonesia from avian flu to 13 and the number who have had bird flu to 20.
Wibisono said the girl died in an Indramayu hospital while her 15-year-old sister and three-year-old brother had been sent to a hospital in Jakarta designated to care for bird flu patients. Indramayu is 175km (110miles) east of Jakarta.
"We found three positive bird flu cases in one family coming from Indramayu, West Java"
director of control of animal-borne diseases
"A lot of fowls died around the neighbourhood where they lived. But we don't know yet whether these fowls were carrying the virus. We sent a team there to investigate this morning," he said, adding that anyone who has had close contact with the children will be tested.
A WHO spokeswoman in Jakarta said she was not aware if a team from the world body would go to Indramayu, but added WHO officials usually joined such investigations with the Health Ministry.
The highly pathogenic strain of bird flu is endemic in poultry in parts of Asia, and has affected birds in two-thirds of the provinces in Indonesia, an archipelago of about 17,000 islands and 220 million people.
In Indonesia, milions of chickens
are kept in backyard barns
The country has millions of chickens and ducks, many in the yards of rural or urban homes, raising the risk of more humans becoming infected with a virus that is confirmed to have killed 79 people in six countries since late 2003.
This includes recent cases in Turkey, the first human infections outside East Asia.
Experts say the H5N1 virus could become more active in the colder months in affected regions.
And there could be more cases in China, Vietnam and elsewhere in East Asia later this month during the Lunar New Year, when chicken will be an integral part of family reunion celebrations.
Trying to build awareness among Indonesian owners of backyard chickens, Red Cross volunteers wearing protective suits went to a village on the outskirts of Jakarta on Monday and showed residents how to keep poultry cages properly cleaned.
Symptoms in Jerusalem
Meanwhile, a patient admitted to a Jerusalem hospital with flu symptoms on Monday is being tested for possible avian flu, a hospital official said.
Bird flu has so far killed 79 people
in six countries since 2003
The man owns chickens, a few of which died in the past few days, so doctors at Jerusalem's Hadassah Hospital decided to test the man's blood for possible avian flu, said Ron Krumer, a hospital spokesman.
Results from the blood samples, which are being tested at the hospital and at the Israeli Health Ministry, were not yet available.