The Department of Agriculture said on Friday that it would begin enforcing rules requiring the spot testing of organically grown foods for traces of pesticides, after an auditor exposed major gaps in federal oversight of the organic food industry.

Spot testing is required by a 1990 law that established the basis for national organic standards, but in a report released on Thursday by the office of Phyllis K. Fong, the inspector general of agriculture, investigators wrote that regulators never made sure the testing was being carried out.

The report pointed to numerous shortcomings at the agriculture department’s National Organic Program, which regulates the industry, including poor oversight of some organic operations overseas and a lack of urgency in cracking down on marketers of bogus organic products.

The audit did not name growers or processors that marketed products falsely labeled organic or say where any such products had been sold.

The head of the National Organic Program, Miles McEvoy, said on Friday that enforcing testing rules was one of several steps the agency was taking to improve oversight of the industry. It will also require unannounced inspections of organic producers and processors and start regular reviews of organic products in stores to make sure they are correctly labeled and meet federal regulations, he said.

“There’s a real commitment from this administration to improve the integrity of this program,” Mr. McEvoy said.

The testing for pesticide residues is expected to begin in September. It will be done by the network of independent certifying agents that are already accredited by the department to inspect and certify organic growers, processors and handlers.