The bird flu virus has now reached Papua, the easternmost part of Indonesia.
About 174 chickens are believed to have died of the H5N1 virus while 414 others have been culled due to suspected infection.
The Jakarta Post reports that tests showed three birds tested were positive for H5N1.
Officers from the Mimika Husbandry Office received a report from a farmer in Sempan village in Timika that his chickens were sick.
They found 40 birds with H5N1 symptoms at the farm.
Inspections of the traditional market also found many chickens with symptoms of the disease.
The market was immediately treated with disinfectant and chickens showing clinical symptoms of infection with the virus were culled to prevent an outbreak.
Officials are still examining where they came from and a circular banning the transportation of chickens out of the regency has been issued.