"It can be a dozen different factors from farm to table" that raise food prices, Johanns said, adding his department anticipates ethanol will only raise food prices 2 percent to 3 percent a year.
Concern is growing among farmers as corn feed normally eaten by cows, chickens and other farm animals is also used for fuel, raising feed prices.
Johanns told the department's annual Outlook Forum in Arlington, Va., he understood ethanol growth was "causing pain for those who rely upon corn to feed animals and as an ingredient in food products."
But he said ethanol would increasingly be made with other feed stocks such as biomass.
Biomass is grown from several plants, including switchgrass, hemp, corn, willow and sugarcane.
Johanns touted the growth of ethanol and biodiesel plants across the country, saying they are "bringing jobs and economic opportunities (to areas) that just a few years ago people were ready to proclaim were dead."
He said the growth of ethanol and biodiesel was creating an increasingly strong "industrial demand" for U.S. agricultural crops.