General Khaled al-Mahjoub, commander of strongman Khalifa Haftar's communications division, said that the containers of uranium had been recovered.
"The situation is under control. The IAEA has been informed," Mahjoub told AFP.
The International Atomic Energy Agency [IAEA] in Vienna reported on Wednesday that 2.5 tons of natural uranium had gone missing from the Libyan location.
Mahjoub added that the containers had been found around three miles from where they had been originally stored in the Sabha area of southern Libya.
In a report to member states on Tuesday, IAEA Director General Rafael Grossi wrote that inspectors found that "10 drums containing approximately 2.5 tons of natural uranium in the form of uranium ore concentrate... were not present."
The IAEA said it was trying to verify the recovery of the uranium on Thursday.
The uranium that had gone missing is a powder consisting of around 80 percent uranium oxide. It is mainly used for the preparation of nuclear fuel for reactors, but it can also be used enriched for use in nuclear weapons.
Western officials have kept a close eye on the situation due to the security and political situation in the North African nation.
The country remains split following the 2011 NATO-backed uprising that removed dictator Moamer Kadhafi's. Libya is now split between an interim government in the capital Tripoli in the west and another in the east, backed by Haftar.
"Missing nuclear material is a safeguards and nuclear security concern, especially given the site is not under the control of the regulatory authority in Libya," a Western diplomat told AFP.