As it reeled from the recall of half a billion eggs for possible salmonella infection, the American egg industry was already battling a movement to outlaw its methods as cruel and unsafe, and adapting to the Obama administration’s drive to bolster health rules and inspections.

The cause of the infections at two giant farms in Iowa has not been pinpointed, Margaret Hamburg, commissioner of the Food and Drug Administration, said Monday in a television interview. But “there is no question that these farms that are involved in the recall were not operating with the standards of practice that we consider responsible,” Ms. Hamburg said in the strongest official indication yet that lax procedures may be to blame.

One of those producers, Wright County Egg, responded that it “strives to operate our farms in the most responsible manner, and our management team has worked closely with F.D.A. through their review of our farms.”

The company, which has also been cited for farm-labor and animal cruelty violations in the past, said that “any concerns raised verbally during F.D.A.’s on-farm visit were immediately addressed or are in the process of being addressed.”