Presidential spokesperson Bheki Khumalo said Mbeki had assured Jones at a meeting on Friday morning that terrorism was very much an issue on the African agenda following the acceptance of the African Convention Against Terrorism by the African Union.
The two men also discussed issues relating to conflict resolution and peace keeping that fell under bilateral military relations, he said.
However, Khumalo added: "The nature of military things is that they do not get discussed".
Jones is a four-star general who previously headed the US Marine Corps.
Under a system of "regional commands", Eucom is also responsible for all American military co-operation and action in Africa - minus the Horn region.
That area falls under Central Command, which is also responsible for prosecuting military operations in Iraq and Afghanistan. – Sapa.
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