International Atomic Energy Agency (IAEA) inspectors on Tuesday found that "10 drums containing approximately 2.5 tons of natural uranium in the form of uranium ore concentrate... were not present" as previously declared at the location, it said.
The site "is currently not under the regulatory control of Libya's state authority," the report said.
The IAEA will conduct "further activities...to clarify the circumstances of the removal of the nuclear material" from the site and investigate the material's "current location", the report said.
Uranium ore concentrate is considered to emit low levels of radioactivity.
But the IAEA cautioned that "the loss of knowledge about the present location of nuclear material may present a radiological risk, as well as nuclear security concerns."
The report did not identify the site or say why Libya was in possession of the material.
Libya under its long-ruling former dictator Moamer Kadhafi had a suspected nuclear weapons programme, which it scrapped in 2003.
But the North African country has been mired in 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.
An inspection of the site had initially been scheduled for 2022 but had to be postponed due to the "security situation in the region," the IAEA report said.
The document said that the location was routinely monitored by the IAEA through commercial satellite imagery and other open source information.
It was through analysing these images that the agency decided to make a physical inspection, despite the security risk and logistical challenge, it said.
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