Barns infested with flies, maggots and scurrying rodents, and overflowing manure pits were among the widespread food safety problems that federal inspectors found at a group of Iowa egg farms at the heart of a nationwide recall and salmonella outbreak.

Inspection reports released by the Food and Drug Administration on Monday described  often in nose-pinching detail  possible ways that salmonella could have been spread undetected through the vast complexes of two companies.

The inspections, conducted over the last three weeks, were the first to check compliance by large egg-producing companies with new federal egg safety rules that were written well before the current outbreak, but went into effect only last month.

“Clearly the observations here reflect significant deviations from what’s expected,” said Michael R. Taylor, deputy commissioner for food for the F.D.A.