But comparing the cost of foods by weight or portion size shows that grains, vegetables, fruit and dairy foods are less expensive than most meats or foods high in saturated fat, added sugars or salt.
Bananas, carrots, lettuce and pinto beans are all less expensive per portion than french fries, soft drinks, ice cream or ground beef.
"Using price per calorie doesn't tell you how much food you're going to get or how full you are going to feel," said Andrea Carlson, scientist at the USDA's Economic Research Service and an author of the study.
For example, eating a chocolate glazed doughnut with 240 calories might not satiate you but a banana with 105 calories just might.
The USDA study criticizes a 2010 report from researchers at the University of Washington. It found that calorie-for-calorie junk food is more cost-effective for low-income people than eating healthy.
Adam Drewnowski, director of the Nutritional Sciences Program at the University of Washington and lead author of the prior study, said he stands by his findings that a healthier diet generally costs more.
"Some of these calories are in fact empty calories, so from the standpoint of nutrition they are not terrific," Drewnowski said. "But the empty calories keep you from being hungry, and this is why people buy them, especially lower-income people."
Margo Wootan, a nutrition advocate with the Center for Science in the Public Interest, said some people don't think they get as much value from fruits and vegetables.
"If they buy a bag of chips for $2, they think it's a good deal, but if they buy a bag of apples for $2, they think it's a lot," Wootan said. "We need to do more to help people understand that fruits and vegetables are not as expensive as they think they are."