The rules were created in response to the nation's first case of mad cow disease in December 2003.
They require that brains, spinal cords and other nerve parts — which can carry mad cow disease — be removed when older cows are slaughtered. The at-risk tissues are removed from cows older than 30 months because infection levels are believed to rise with age.
The Agriculture Department said Monday it had cited beef slaughterhouses or processing plants 1,036 times for failing to comply with rules on removing those tissues, which are commonly called specified risk materials or SRMs. The violations occurred over 17 months, ending in May.
The number of violations amounts to less than 1 percent of all citations at those plants, said USDA spokeswoman Lisa Wallenda Picard.
"At no point in time did SRMs get to consumers," Picard said. "There was not one example of that."
The department released the information in response to requests made by several groups under the federal Freedom of Information Act. The records were from January 2004, when the rules went into effect, through May of this year.