Iran, trying to keep its F-14s able to fly, is aggressively seeking components from the retired US Tomcat fleet.
The Pentagon's surplus sales division, the Defense Reutilization and Marketing Service, told investigators the parts were sold because it failed to update an automated control list and remove the aircraft parts before they were listed on its Internet sales site.
The GAO's investigation focused on F-14 parts.
"One country with operational F-14s, Iran, is known to be seeking these parts," Greg Kutz, the GAO's managing director of special investigations, wrote in the report. "If such parts were publicly available, it could jeopardize national security."
A Democratic senator said the investigation shows why legislation he proposed that would ban the sale of all F-14 parts is needed.
"The Pentagon's system is still riddled with holes," Senator Ron Wyden of Oregon said in a telephone interview. "These are the very parts that they said they wouldn't be selling and they still are, and so you've got to make sure the changes are going to actually have teeth and work."
The Defense Department said in January that it was suspending sales of all F-14 parts, including those that could be used on multiple types of aircraft, while the Pentagon reviewed security.
The new GAO report was released as a surplus dealer trade association accuses the Pentagon of overreacting to security concerns and wasting taxpayer money by junking thousands of items unrelated to the F-14.
The Defense Department said the allegations are not true. The surplus dealers want Congress to force the Pentagon to do a better job separating sensitive scrap from items that are safe to sell.
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