SEOUL, June 4 (Reuters) - South Korea halted beef imports from plants owned by Cargill [CARG.UL] and Tyson Foods Inc. <TSN.N> after determining the meat they shipped violated an export agreement with Washington, the agriculture ministry said on Monday.

After South Korea lifted a 3-year-old a ban on U.S. beef imposed due to mad cow disease, the two countries agreed in September 2006 only certain cuts of boneless beef could be sent to South Korea and they had to be designated for export only.

Last week, South Korea suspended beef imports from two Cargill plants after the discovery of bone in beef cuts.

The U.S. Department of Agriculture said in response to an inquiry from Seoul that 66.4 tonnes of 118 tonnes of beef shipped to South Korea, including the meat from Cargill, were actually intended for U.S. sale, not export.

"We asked Washington to explain how the government issued export quarantine certificates for the beef and to step up its efforts to ensure safe beef exports," the ministry said in a statement.

South Korea will return the 66.4 tonnes of beef and will temporarily ban imports from two plants owned by Cargill and two by Tyson.

South Korea, once the third-largest importer of U.S. beef, accepted in April the first shipment of boneless meat into the country for sale since December 2003.

The country has been expected to be ready by September to resume imports of U.S. beef with bones, while Washington has called on Seoul to ease import restrictions to ease the passage of a bilateral trade deal.

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