A health ministry official says the child, from Jakarta’s western suburbs, was admitted to hospital on Thursday and died hours later.
The results of the local test will now be sent to a World Health Organisation (WHO) laboratory for confirmation.
Bird flu (H5N1 strain) has already killed 41 people in Indonesia and 131 people world wide.
A World Health Organisation laboratory test has confirmed a 5-year-old Indonesian boy who died last month was infected with bird flu.
Human cases generally stem from contact with infected birds.