The disease erupted at farms in Chak Shahzad, a suburb of Islamabad, this week. Officials said there was no case of human infection by the H5N1 virus.
"The disease at the three farms killed 6,000 birds and we culled the remaining 5,000 on Tuesday," Agriculture and Livestock Ministry spokesman Mohammad Afzal told AFP.
"The surrounding farms have been advised to immediately implement vaccination," he said.
Afzal said all workers on the affected farms were examined by the ministry of health but "none was found affected by the virus."
The disease last appeared in April in northwest Pakistan and the southern port city of Karachi, but it was quickly controlled.
The authorities in March were forced to shut an Islamabad zoo and slaughter dozens of birds, after the virus was found in peacocks and geese.
Pakistan produces 4.5 million chickens annually.