Japan had only imported poultry from North Korea once during the past five years, when some five tonnes was imported in 2002. Chicken consumption in Japan was about 1.74 million tonnes in 2002/03.
Japan as a rule halts poultry imports from countries where there has been an actual or reported outbreak of bird flu.
Quoting an unnamed source, South Korea's Yonhap news agency had said on Tuesday the chickens died at a poultry farm in Pyongyang, prompting an emergency response from North Korean authorities.
The outbreak has not been independently verified.
Yonhap said it was not immediately clear if the outbreak was restricted to the farm, believed to be the largest in the country and located in the western part of Pyongyang.
It was also not clear if the strain of virus involved was H5N1, which can jump from birds to humans and is deadly.
That strain of the virus has killed 34 Vietnamese, 12 Thais and one Cambodian since it swept across large parts of Asia in late 2003.
Yonhap said North Korean authorities had buried the dead chickens but that some residents had dug up the poultry to sell.