The French ministry statement did not explain how the missiles were lost and the find is likely to boost suspicions that Paris was backing Haftar on the ground in their offensive on Tripoli.
France admitted Wednesday its missiles had been found at a Libyan base used by forces loyal to Khalifa Haftar, in an embarrassing admission that raises fresh questions about its role in the conflict.
Confirming a report in the New York Times, a defense ministry statement said the U.S.-made Javelin missiles discovered in June at a camp south of Tripoli had been purchased by France.
But it denied supplying them to Haftar in breach of a UN arms embargo, saying French forces operating in the war-torn country had lost track of them after they were judged to be defective.
"Damaged and out-of-use, these weapons were being temporarily stocked in a warehouse ahead of their destruction," it said. "They were not transferred to local forces."
The anti-tank missiles, worth US$170,000 each, were seized when forces loyal to the UN-recognized government in Tripoli overran the pro-Haftar base in Gharyan, 100 kilometers south of Tripoli.
Three of them were shown to journalists on June 29 alongside Chinese-made shells bearing the markings of the United Arab Emirates (UAE).
"These weapons were for the protection of forces undertaking intelligence and counter-terror missions," the French statement said.
Haftar's opponents have argued he was a warlord and dictator-in-the-making, while the military strongman is backed by some Western and a few regional countries, claiming he was a bulwark against Islamist groups.
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.
France's role has caused tensions since Macron threw himself into diplomatic efforts to resolve the conflict after his election in May 2017, seeing the instability as a major 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.