The dead pigs were found in an upstream area of the river, which serves as a drinking water source for Shanghai residents, Xinhua News Agency reported.
The water quality was not affected, the city's water supplies bureau said, but authorities are doing additional testing to ensure its safety.
Authorities are investigating a bio-safety treatment on the dead pigs and are looking into where they could have come from, Xinhua said.
There are no reports of animal epidemics in the city.
As of Saturday, more than 900 were removed, but authorities are still retrieving the pigs from the river, Xinhua said.