The orders come after tens of thousands of birds have already been killed in what government officials describe as one of the Himalayan nation's worst outbreaks of avian flu.
Some 62 cases of bird flu have been recorded at 250 poultry farms in three districts in the past few weeks, officials said.
Officials at Directorate of Animal Health said the government ordered the cull to be stepped up in the wake of a failure to control the H5N1 virus after imposing a week-long ban on the sales of poultry products.
"Now, the poultry farmers have joined us in our battle. We are sure we will control it," he said.
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Nepal's first outbreak of bird flu was in January 2009.
H5N1, a common strain of bird flu, has killed 377 people globally between 2003 until July 5 this year, according to the World Health Organisation.
No human deaths from bird flu have been reported in Nepal.