The ministry said post mortem analyses had confirmed the presence of the deadly H5N1 virus in the bodies of a 15-year-old boy from West Java, a 22-year-old woman from the city of Palembang, on the island of Sumatra, and a 39-year-old man from the city of Surabaya, the capital of East Java.
Since 2003, 89 people have been infected with the virus in Indonesia, 69 of whom subsequently died. Indonesia has the world's highest death toll from bird flu.
In a related development following progress made in the protocol for the exchange of virus cultures between laboratories around the world, Indonesia has resumed sending specimens of the bird flu virus to the World Health Organization (WHO) after a four-month hiatus that many feared would put the world at greater risk of a pandemic.
The standoff was caused by the Indonesian Health Ministry's insistence that the world health body change its system for sharing virus samples, in which it collects specimens from around the world and distributes them to vaccine makers and other researchers.
The ministry has for the past four months refused to share samples without a guarantee they would not be used by drug companies to produce vaccines unaffordable to developing countries.
The resumption was agreed to at recently concluded high-level talks in Jakarta on the bird flu virus, known as the WHO High-level Technical Meeting on Responsible Practices for Sharing Avian Influenza Viruses and Resulting benefits.
The virus, which was first isolated in humans in 1997, has been spreading rapidly, resulting in the deaths and culling of millions of birds, and a human death toll approaching 200.
Although the virus has so far been mainly restricted to animals, many scientists fear that it could mutate into a form transmissible between humans, unleashing a catastrophic global pandemic similar to the Spanish flu outbreak of 1918 that killed millions around the world.
In March, bird flu was detected at several poultry farms in the Moscow region. The area was quickly sealed off and the outbreak contained.
