Officials found the H5N1 strain of bird flu at a poultry farm on the outskirts of the city, where it was first detected 10 months ago.
"Around 1,200 chickens had died from bird flu virus in a poultry farm," said Narayan Prasad Ghimire, a senior veterinary officer at the Directorate of Animal Health.
"We have killed the remaining 800 chickens and destroyed thousands of eggs," he said, adding that his team was conducting surveillance of the affected area.