Confirming a report in The New York Times, the Army Ministry said in a statement that the missiles were intended for the "self-protection of a French military unit deployed to carry out counterterrorism operations."
"They were not transferred to local forces," the statement said.
"Damaged and unusable, the armaments were being temporarily stocked at a depot ahead of their destruction," the ministry said.
The anti-tank missiles, worth $170,000 (150,000 euros) each, were seized when forces loyal to the U.N.-recognized government in Tripoli overran the pro-Haftar base in Gharyan, 100 kilometers (60 miles) south of Tripoli.
Three of them, as well Chinese-made shells bearing the markings of the United Arab Emirates (UAE), were shown to journalists including AFP reporters on June 29.
The ministry statement did not explain how the missiles were lost.
The find could boost suspicions that Paris is backing Haftar on the ground.
Claudia Gazzini, senior Libya analyst at the International Crisis Group, an NGO, said the town of Gharyan had in the past housed facilities for obsolete weapons.
But she said there were unanswered questions about whether French troops were present when the base was overrun.
"The French need to clarify in greater detail," she told AFP. "The open question is whether or not they are actively supporting Haftar forces in their offensive on Tripoli."
Haftar has been branded a warlord and dictator-in-the-making by his opponents.
On April 4, he launched an offensive on the Libyan capital seeking to overthrow the government of Prime Minister Fayez al-Sarraj.
The fighting has claimed at least 1,000 lives and displaced tens of thousands of people.
In a video distributed by pro-Sarraj forces, a captured pro-Haftar commander alleges six French military advisers and UAE soldiers were at the base in Gharyan when it was overrun.
This was dismissed as "fake news" by the French embassy in Tripoli.
France under President Emmanuel Macron has publicly denied taking sides in the conflict and has called for a U.N. arms embargo to be enforced.
French special forces and members of its DGSE intelligence service are, however, known to be operating in Libya, which descended into chaos after a 2011 uprising and NATO-backed military campaign against late dictator Muammer Kaddafi.
"These weapons were for the protection of forces undertaking intelligence and counter-terror missions," the French statement said.
The Libyan conflict has drawn in a range of regional and international actors and the country is awash with foreign weaponry despite the U.N. embargo.
"Before, the violations were happening but people were still cautious," Gazzini told AFP. "But now it is quite the contrary. There is no shame in boasting about the arrival of new equipment."
Analysts say Haftar has been backed by Saudi Arabia, the UAE, Egypt, Russia, the U.S. and France during offensives against Islamist militias that have brought most of the country under his control.
The U.N.-recognized government in Tripoli headed by Sarraj controls a much smaller section of territory around Tripoli in the west and draws support from Turkey, Qatar and Italy, analysts say.
France's role has caused tensions.
Macron threw himself into diplomatic efforts to resolve the conflict after his election in May 2017, seeing the instability as a major security worry and a source of migration to Europe.
He invited Haftar and Sarraj to a peace conference in Paris in 2017 which was seen as giving the commander international legitimacy for the first time.
The UAE has also denied shipping weapons to Haftar's forces in Libya.
Before the latest discoveries, U.N. experts were investigating so-called Chinese Blue Arrow missiles fired from a Chinese drone in a suburb of Tripoli in April which experts suspect were supplied by the UAE.
Libya has remained beset by turmoil since 2011 when a bloody NATO-backed uprising led to the ouster and death of long-serving President Gaddafi after more than four decades in power.
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