International Atomic Energy Agency (IAEA) chief Rafael Grossi told the organisation's member states that inspectors on Tuesday found that 10 drums containing uranium ore concentrate "were not present as previously declared" at the location in Libya.
The IAEA will conduct further activities "to clarify the circumstances of the removal of the nuclear material and its current location", it said in a statement, without providing further details on the site.
Libya in 2003 abandoned a programme to develop nuclear weapons under its long-ruling former dictator Moamer Kadhafi.
The North African country has been mired in a political crisis since Kadhafi's fall in 2011, with a myriad of militias forming opposing alliances backed by foreign powers.
It remains split between a nominally interim government in the capital Tripoli in the west, and another in the east backed by military strongman Khalifa Haftar.
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