He asked village-level officials to ensure no corpses were thrown into water and said the state government would pay poor families 5,000 rupees ($68) each to cremate or bury the bodies of the dead.
The state has also asked police to patrol rivers to stop the practice.
India has been officially reporting about 4,000 daily deaths from the disease for nearly two weeks, but health experts say the toll is probably much higher because of factors such as poor testing in rural areas.
The jump in deaths has led to backlogs at crematoriums in many places and multiplied the cost of last rites. On Saturday, Uttar Pradesh spokesman Navneet Sehgal denied media reports that as many as 2,000 corpses of possible virus victims had been pulled from rivers in the state and neighbouring Bihar in recent days.
"We keep recovering 10 to 20 bodies every now and then," Sehgal told Reuters, adding that some riverside villages did not cremate their dead due to Hindu traditions during some periods of religious significance. Bihar officials did not respond to requests for comment.