Kbec Vina Ltd. has also been suspended for discharging wastewater for 4.5 months.
The yellow sewage, which has an unpleasant smell, was found flowing from the company's landfill to nearby streams in February.
The company said the sewage had been treated, but tests found its nitrogen concentration was more than 50 times permitted levels, and with a chloride concentration of more than 10 times permitted levels.
The company, which treats industrial and household waste in the province by burying it, was fined nearly VND700 million in 2008 for a similar violation.