Residents found the dead ducks in Nanhe river in Pengshan county, Sichuan province, and alerted the environmental department, reports the BBC.
Local residents and livestock are not at risk, as the river was not used for drinking water, officials added.
The news comes as the toll of dead pigs pulled from Shanghai's Huangpu river passed 16,000.
Liang Weidong, a deputy director in Pengshan's publicity department, said that the authorities were first made aware of the ducks on Tuesday.
Officials discovered over 50 woven bags containing the carcasses of around 1,000 ducks in the river, some of which were already decomposed.
Liang said they were unable to determine the cause of death, and added that the bodies had been disinfected and buried.
The news has prompted concern and criticism from some users on weibo, China's version of Twitter, with many expressing incredulity at the government's assurance that the water is safe.
Weibo user If So said the dead ducks in Pengshan river presents a very practical problem, and shows how the society's bottom line is getting lower and lower.
Earlier, Shanghai's municipal government pulled out 16,000 pig corpses from Huangpu river, which supplies drinking water to Shanghai. It is still not clear where the dead pigs came from.
--ANI (Posted on 26-03-2013)