Outbreaks were confirmed in two villages in West Bengal, which has been severely hit by the virus in previous years, a government statement said late Tuesday.
Samples tested positive for the H5 strain of avian influenza, popularly known as bird flu.
All chickens will be culled within a three kilometre (nearly two mile) radius of the focal point of the infection, the statement said, without giving numbers.
Eggs and chicken feed will also be destroyed to control the further spread of the disease.
The Indian outbreak of flu follows a warning three weeks ago by the UN Food and Agriculture Organisation that avian flu was on the rise globally after a five-year decline.
The FAO said a mutant strain of the H5N1 virus was spreading in Asia and outside the continent.
It was not immediately known whether there was any link between the Indian outbreak and the mutant strain detected in China and Vietnam, for which no vaccine has yet been developed.
If it spreads to humans, bird flu can cause fever, cough, sore throat, pneumonia, respiratory disease and sometimes death.
In 2008, West Bengal carried out a massive cull of nearly four million birds to bring bird flu under control.
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