Culling operations are on in and around Ravangla in Sikkim.
State Animal Husbandry Department sources report that the operations are expected to last for four to five days. Nine Rapid Response Teams have been deployed to complete the operations.
Officials in Sikkim said they would initially cull an estimated 15,000 chickens and ducks.
Earlier, hundreds of thousands of birds had been culled in Assam and neighboring Meghalaya after bird flu was detected in November last year.
Experts have warned that the H5N1 virus might mutate or combine with the highly contagious seasonal influenza virus and spark a pandemic that could kill millions of people across the world.
WHO had described a January 2008 outbreak of bird flu in West Bengal, when more than four million birds were culled, as the worst ever in India.