According to official reports samples have been sent to laboratories in Bhopal and some have tested positive for the H5N1 stain.
"We have started culling the birds, till now we have found 61 birds with the infection, we have killed them and buried them also," said Moloy Bharali, a culling officer.
Culling officers are going from house to house urging the villagers to hand over their poultry.
The villagers have also been promised a compensation of 20 rupees per chicken, 50 rupees per hen, 35 rupees for a duckling and 70 rupees for a duck.
Villagers like Mohammad Muktar though initially reluctant, gave away their poultry when culling officers made them understand the consequences.
"We are dependent on these birds and chickens for a livelihood. Poor people like us sell the eggs and make a livelihood and if these birds are killed, we will make huge loses, but we have given the birds to the officers because we understand that it would be dangerous if the infection catches human beings," said Muktar.
According to official reports, over 30,000 chickens and ducks would be slaughtered in the next three days in 20 villages, after one of them was hit by bird flu.
India has not reported any human infections so far, though the first outbreak in poultry was reported in 2006 in Maharashtra.
Expert's fear the H5N1 strain could mutate into a form easily transmitted from person to person, leading to a pandemic.