The UN's International Atomic Energy Agency (IAEA) has told the organisation's member states that 10 drums containing uranium "were not present as previously declared" at the location in Libya.
The missing uranium stockpile could pose radiological risk and security concerns, the agency has said.
The IAEA sounded the alarm after a visit by its inspectors to the undisclosed site earlier this week, where it found less uranium than originally reported. Currently, officials are working to locate the 2.3 missing tonnes.
"The loss of knowledge about the present location of nuclear material may present a radiological risk as well as nuclear security concerns," the IAEA said, adding that reaching the site required "complex logistics".
It is unclear when the uranium went missing or who could have taken it.
Natural uranium cannot immediately be used for energy production or bomb fuel. However, each ton of natural uranium – if obtained by a group with the technological means and resources – can be refined to 12lb of weapons-grade material over time, experts say.
This process typically requires the metal to be converted into a gas, then later spun in centrifuges to reach the levels needed.
Libya renounced its nuclear, chemical and biological weapons programme in 2003, following secret discussions with the USA and the UK.
Nonetheless, since Gaddafi's fall in 2011, the country has been beset by political crises and competing militias forming opposing alliances backed by foreign powers. Political control in the country 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.
The missing uranium was removed from a site in Libya not under government control, which will make its recovery difficult. The IAEA declined to offer more details about the location, but a likely option is Sabha, 410 miles south-east of Tripoli.
While inspectors removed the last of the enriched uranium from Libya in 2009, thousands of barrels of so-called yellowcake uranium remained behind, with the UN in 2013 estimating 6,400 barrels were stored at Sabha.
The barrels had been gathered by Gaddafi for a once-planned conversion facility that was never built in his decades-long secret weapons programme.
"Stressing that Libya viewed the question as primarily a commercial one, [the official] noted that prices for uranium yellowcake on the world market had been increasing, and that Libya wanted to maximise its profit by properly timing the sale of its stockpile," then-ambassador Gene A Cretz wrote.
Inspectors had wanted to visit the location last year, but the trip had to be postponed because of fighting between rival Libyan militias.
In 2013, UN experts reported that weapons smuggled out of Libya were fuelling conflicts in other parts of Africa and the Middle East.
