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The farmers are to be compensated with Rs 100 each for ducklings and chickens less than 2 months old, and Rs 200 each for those above 2 months.
The culling will be carried out in select places in Ambalapuzha, Edathua and Thakazhi.
The meeting pointed out the need to strengthen awareness among farmers in the district as part of measures to stop the spread of bird flu.
Alappuzha is the only place in the country where instances of bird flu have been reported continuously for the last 10 years.
The US Centre for Disease Control and Prevention has already cautioned doctors to treat cases occurring in individuals closely associated with birds and livestock with utmost seriousness.
The District Collector has imposed a ban on the consumption and sale of duck and chicken till April 25.
Authorities have initiated plans to cull all farm birds within a one-kilometre radius of the affected area.
Bird flu was confirmed on January 6 as tests were done after several ducks in a farm at Kattikkunnu area of Chembu died.
Around 8,000 ducks and domesticated birds within one-km radius of the hotspot will be culled in the coming days to check the disease spread.
In India, bird flu or avian influenza is spread mainly by migratory birds coming into the country during the winter months between September and March. The disease is zoonotic.