Shut down follows claims the miller has been discharging toxic waste in River Kibos which drains into Lake Victoria.
Kisumu Woman Representative Rozah Buyu cautioned against blanket condemnation, saying the firm has employed many local residents.
The National Environment Management Authority (Nema) has shut down two plants at Kibos Sugar Company in Kisumu over alleged pollution.
This follows claims the miller has been discharging effluent to River Kibos which drains into Lake Victoria.
On Monday, Kisumu County Nema director Tom Togo told Nation they had stopped operations of a distillery and paper mill plants in the factory.
“The two plants were responsible for the discharge of effluent into the local river. Until they comply, the two plants shall remain shut,” Mr Togo said.
Residents have been up in arms against the factory, saying the effluent dumped into the river was harmful to them and their livestock.