Critics of a renewable fuel standard said higher corn prices and a weak harvest due to drought meant the government should waive requirements on ethanol blends for gasoline.
The EPA, however, said it looked at economic analysis from the U.S. Department of Energy and Department of Agriculture and found no cause for alarm.
"We recognize that this year's drought has created hardship in some sectors of the economy, particularly for livestock producers," Gina McCarthy, an EPA administrator, said in a statement. "But our extensive analysis makes clear that congressional requirements for a waiver have not been met and that waiving the RFS will have little, if any, impact."
Advanced Ethanol Council Director Brooke Coleman said the EPA's decision was the right one.
"Waiving the RFS would have done little if anything to reduce grain prices but would have hurt consumers at the pump and undercut investment in advanced biofuels," he said in a statement.
The EPA in 2013 calls for 13.8 billion gallons of ethanol to be blended into gasoline, a 4.5 percent increase from this year.