The weather in the area has been cold and wet, leading authorities in the populous province to the reach an initial conclusion that the young birds fell ill and died of coccidiosis, an intestinal parasite, Wen Wei Po reported.
Farmers in the area, however, were sceptical because they said coccidiosis was common and unlikely to kill so many chicks at once, the newspaper reported.
Nearly 3,000 surviving chicks on the farm were culled and incinerated, it said.
The bird deaths come at a time when H5N1 avian flu is spreading around the world, prompting health experts to warn about a possible pandemic.
Guangdong has yet to report any outbreaks of H5N1, but several birds, mostly wild, have been killed by the disease in neighbouring Hong Kong.
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