Meat of ruddy shelduck and larger whistling duck along with a country boat were seized from them, divisional forest officer (Chilka) Bikash Ranjan Das said.
They might have trapped the birds in the lake. The meat was probably processed after the kill because it was packed in a tiffin box, range officer (Tangi) Ashok Das said.
He said the duo, arrested on Saturday, was involved in bird poaching cases earlier.
Halu Behera (55) and his son Jayaguru (30) of Mangalajodi were caught when they were returning in a boat after killing two migratory birds.
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On February 15, wildlife personnel arrested four persons and seized 12 dead birds from them from Kankanakuda.
With this, over 100 migratory birds have been killed by the poachers in Chilika in the last two months.
Altogether 23 people were arrested on charge of hunting migratory birds, officials said adding bird poachers were active in the lake as there is a huge demand for the meat of waterfowls in nearby towns.