Just one of the Cobalt-60 sources, as small as a paintbrush, could kill someone directly exposed within minutes, the announcement said.
International experts figures it was just too dangerous to keep that much radioactive material in a country as volatile as Lebanon.
The agency sought to remove the material in 2006, but was thwarted when war broke out between Hezbollah and Lebanon.
"Given the political situation in the Middle East and particularly in Lebanon, we saw this source as vulnerable to malicious acts," said. Robin Heard, the scientist who oversaw the mission. "If it was stolen, it could cause a lot of damage to people."
The Cobalt-60 came from an irradiator used in an agricultural project 10 years ago.
Heard said keeping the material in Lebanon "posed some threat, actually a lot of threat on the public, on Lebanon."