The admission raises fresh questions about the role of France in the conflict.
A defence ministry statement, confirming a report in the New York Times, said the US-made Javelin missiles discovered in June at a camp south of Tripoli had been purchased by France.
But the ministry 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 150,000 euros each, were seized when forces loyal to the UN-recognised government in Tripoli overran the pro-Haftar base in Gharyan, 100 kilometres south of Tripoli.
The French ministry statement did not explain how the missiles were lost and the find is likely to boost suspicions that Paris is backing Haftar on the ground.
The French statement said the weapons were "for the protection of forces undertaking intelligence and counter-terror missions."
Haftar's opponents have branded him a warlord and dictator-in-the-making, but the military strongman is backed by some Western and many regional countries as a bulwark against Islamist groups.
On 4 April, he launched an offensive on the Libyan capital seeking to overthrow the government of Prime Minister Fayez al-Sarraj.
Tens of thousands displaced
The fighting has claimed at least 1,000 lives and displaced tens of thousands of people.
France under President Emmanuel Macron has publicly denied taking sides in the conflict and has called for a UN arms embargo to be enforced.
The Libyan conflict has drawn in a range of regional and international actors and the country is awash with foreign weaponry despite the UN embargo.
Analysts say Haftar has been backed by Saudi Arabia, the UAE, Egypt, Russia, the US and France during offensives against Islamist militias that have brought most of the country under his control.
The UN-recognised government 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.