Yet no larger action was taken. Food and Drug Administration officials insisted as recently as last week that they were surprised by the outbreak because Mexican peppers had not been spotted as a problem before.
But an Associated Press analysis of FDA records found that peppers and chilies were consistently the top Mexican crop rejected by border inspectors for the last year.
Since January alone, 88 shipments of fresh and dried chilies were turned away. Ten percent were contaminated with salmonella. In the last year, 8 percent of the 158 intercepted shipments of fresh and dried chilies had salmonella.
On Friday, Dr. David Acheson, the FDA's food safety chief, told reporters peppers were not a cause for concern before they were implicated in the salmonella outbreak.
"We have not typically seen problems with peppers," Acheson said. "Our import sampling is typically focused on areas where we know we've got problems or we've seen problems in the past, which is why we're now increasing our sampling for peppers."
On Monday, the FDA said Acheson's comment was in relation to outbreaks or illness associated with Mexican peppers, not the rejection of pepper shipments at the borders. Calls to the FDA seeking elaboration were not immediately returned.
Still, food-safety advocates question why the agency did not pay more attention to the peppers being stopped at the border and why it took the nation's largest foodborne illness outbreak for the agency to ratchet up its screening of companies known for shipping dirty chilies.
"If the fact that they were showing up on problem lists for a year doesn't make them high-risk, I don't know what does," said Ami Gadhia, policy counsel with Consumers Union, the nonprofit publisher of Consumer Reports magazine. "If it's across the board, then that's a systemic problem that FDA needs to be able to nimbly respond to."
The agency initially suspected that fresh tomatoes had caused the outbreak. Then officials determined in mid-July that jalapenos could also be sickening people and eventually traced implicated pepper shipments all the way back to two farms in Mexico.
The agency doesn't keep count of what percentage of the nearly 491,200 metric tons of Mexican peppers imported last year were turned away at the U.S. border. In general, the federal government inspects less than 1 percent of all foreign food entering the country.
According to the Department of Agriculture, 84 percent of all fresh peppers eaten in the U.S. come from Mexico.
In the last year, the agency's data shows that dozens of cases were turned back due to filth, illegal pesticides and in one case, something poisonous.
Bob Buchanan, a former senior science adviser at FDA, said part of the problem may be that the agency sets its priorities for the food it considers to be high-risk years in advance.
Dried peppers and other imported spices were considered sufficiently risky to be mentioned on a 2006 FDA manual instructing inspectors on which high-risk foods deserved a more careful check.
The agency has long considered salmonella to be a risk in dried chilies, since foreign spice traders often leave peppers to dry in the sun where they're vulnerable to contamination from birds and other animals, Buchanan said.
Inspectors might have looked over the odd box of fresh Mexican chilies, but no one paid raw peppers much attention since they were not mentioned as a high-risk crop, he said.
"Somebody could have picked up a box and looked at peppers if they wanted to, but I'm not sure that would have been a high priority," Buchanan said. "It would require a big leap to think that salmonella in dried peppers could be related to problems in fresh chilies."
Since the salmonella outbreak began in April, 1,423 people have fallen ill and the produce industry has lost more than $200 million as consumers have shied away from buying fresh produce.
Federal investigators are now focusing their probe on fresh hot peppers from Mexico — jalapenos and serranos — but still suspect that tainted tomatoes were initially involved.
This month, the agency put a dozen Mexican growers or distributors on its "import alert" list for tougher border screening.
On Friday, Acheson said the agency had stepped up testing of certain Mexican produce and uncovered more cases of salmonella contamination — just not the same strain that caused this particular outbreak — in jalapenos, basil and cilantro.
In July, six separate shipments of fresh jalapenos and serranos were stopped after inspectors found they were contaminated with salmonella, FDA data shows.
One crate detained on July 29 came from Agricola Zaragoza, a Mexican packinghouse that handled produce from two farms where chilies linked to the outbreak were traced.
"If so many of the peppers we eat in the U.S. come in from Mexico, you'd think we would want to pay more attention," said Mike Doyle, director of the University of Georgia's Center for Food Safety, which works with industry to improve growing and packing practices. "Something isn't working."