Eleven more buffaloes fell ill after drinking water from the river and were being treated by veterinar.
The incident took place on Friday evening.
Ramakant, a local resident who had filed a police complaint, said: "About 42 buffaloes from Tara Ka Purwa village had gone to graze along a drain in Devsthan locality, Chinhat. The buffaloes started falling unconscious after drinking water from the drain.
"The effluents from the factory discharged into the drain probably contained some poisonous substance. We found 28 buffaloes dead and 11 seriously ill. We shifted the ill ones to veterinary hospital. Several buffaloes are still missing. We suspect their disappearance is an attempt to cover up crime."
Chinhat SHO, Sachin Singh said a case has been lodged against Vishal Swarup Agarwal, owner of India Pesticide Limited, on the complaint of Ramakant.
"We will take action once test reports come," he said.
The locals also complained of irritation and nausea after the incident.
"A putrid smell from the drain has spread to even far off colonies," the residents said
Following the incident, the Indian Institute of Toxicology Research (IITR) rushed a team of scientists to collect water samples on Saturday.
IITR director, Professor Alok Dhawan said: "We have collected samples to test toxicity and pollutants in the water."
The Uttar Pradesh Pollution Control Board also sent samples to a laboratory to find reason for bovine deaths.
( With inputs from IANS )