The agency called spice contamination “a systemic challenge” and said most of the insects found in spices were the kinds that thrive in warehouses and other storage facilities, suggesting that the industry’s problems result not from poor harvesting practices but poor storage and processing.

John Hallagan, a spokesman for the American Spice Trade Association, said Wednesday that he had not seen the report, so he could not comment on it. But spice manufacturers have argued in the past that food manufacturers often treat imported spices before marketing them, so F.D.A. findings of contamination levels in its import screening program do not mean that spices sold to consumers are dangerous.

F.D.A. inspectors have found that some spices that claim to have been treated are contaminated nonetheless. And the high levels of filth from insects and rodents is a problem that is not easily resolved because, unlike with salmonella contamination, simply cooking or heating the spices will not rid the products of the problem. Insects can also be a source of salmonella contamination.

What share of the nearly 1.2 million annual salmonella illnesses in the United States result from contaminated spices is unclear, officials said. Fewer than 2,000 people had their illnesses definitively tied to contaminated spices from 1973 to 2010, and most people eat spices in small quantities. But people often fail to remember eating spices when asked what foods might have sickened them, so problems related to spices could be seriously underreported, officials said.

Recent legislation in the United States grants the F.D.A. the power to refuse entry of foods that the agency even suspects might be contaminated — strong leverage to demand changes in harvesting, handling and manufacturing practices in foreign countries.