Samples were sent to laboratories in Bhopal and have tested positive for H5N1 avian influenza.
The State Government has ordered culling operations and culling officers have already started going from house-to-house urging the villagers to hand over to them their poultry.
"Cases of bird flu were reported ten days back, but the laboratory has confirmed now. The epicentres have been confirmed. The bird flu operation has been started," said Mukul Das, a culling official.
Villagers like Montu Ali in Kamrup district were reluctant to give away their poultry in spite of the culling officers making them understand the consequences of the virus spreading further.
"They say that they will pay us Rs 20 per bird, but the market price is Rs 22 per bird. This is not justified; we depend on these farms for a livelihood. I don't know what to do. We are not even being given money; they are giving us receipts, ," said Ali, a poultry farm owner.
Sale and movement of poultry in and around Guwahati has been prohibited and precautionary measures stepped up in other parts of the state.
Health workers have moved to affected areas to check people for any flu-like symptoms.
India has not reported any human infections so far, though the first outbreak in poultry was reported in 2006 in Maharashtra.