Nearly 9,000 dead pigs were fished out of the Huangpu river in Shanghai, and 3,600 others from rivers and lakes in Jiaxing, with the search continuing in both cities, 'The South China Morning Post' quoted government sources as saying.
Authorities have also found traces of a common pig virus in some of the animals floating in the Huangpu River this week.
"Shanghai's animal control authority found 'porcine circovirus', a common disease among hogs that was not known to infect humans, in 13 of 20 samples of internal organs taken from dead pigs retrieved from the Huangpu," the newspaper quoted Ministry of Agricultural as saying.
Both Shanghai, a city of 23 million people, and Jiaxing say there's been no swine epidemic and that tap water remains safe, but local residents remain worried about water contamination.
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Officials in Shanghai has blamed farmers in neighbouring Zhejiang province for throwing pigs, suspected to have died of disease, into the river upstream, although officials from the area have admitted to only a single producer doing so.
Authorities also said that after intensified checks they have not found any substandard pork products in the market and were closely monitoring the situation.
A total of 130,000 households raised more than seven million hogs in Jiaxing last year - with 89 per cent of them running small farms with capacity for fewer than 50 pigs.
Earlier in 2008, China faced one of its biggest food-safety scandals when the industrial chemical 'melamine' was found to have been illegally added to dairy products, killing at least six babies and 300,000 falling sick.