The National Bureau of Investigation said it launched the "unprecedented" operation in mid-October following a tip-off from the government's Philippine Nuclear Research Institute, which warned the group posed a threat to national security.
Raids of four addresses in Manila and the central and southern Philippines led to the arrests of a man, his female partner and a second male suspect, and the recovery of 100 kilograms of metal bars, rocks and black powder that tested positive for Uranium-235 and Uranium-238, the bureau said in a statement.
It was unclear how the group obtained the depleted uranium, a material which the International Atomic Energy Agency website says may be used as fuel for certain types of nuclear reactors and nuclear weapons.
The group was attempting to sell the materials to the public by misrepresenting them as "precious metals", it added.
The bureau said the uranium also contaminated two of the raided addresses.
One of them "is currently undergoing decontamination procedure before its release to the owners", the statement said.
The bureau said the suspects were charged with unlicensed ownership and trade of atomic energy materials, punishable by a five-year prison term.
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