The navy, which has two frigates deployed in the area, detected "multiple drone attacks originating in Yemen" overnight Monday to Tuesday, before destroying two of the unmanned aircrafts, the ministry said.
The attack came a day after the European Union formally launched a naval mission to protect Red Sea shipping from the Iran-backed Huthis who control much of war-torn Yemen.
The rebels have been harassing the vital shipping lane since November in a campaign they say is in solidarity with Palestinians in Gaza during the Israel-Hamas war.
The European Union aims to have the mission -- called Aspides, Greek for "shield" -- up and running in a "few weeks" with at least four vessels, an official said on Friday.
France has deployed the Alsace, a frigate with air defence capabilities, and the Languedoc, an anti-submarine frigate, in the area.
The Languedoc previously shot down two drones in the Red Sea in self-defence in December, the foreign ministry said.
On Tuesday evening, the Huthi's military spokesman Yahya Saree said they had "carried out a military operation using several drones against a number of enemy American warships".
The United States is already spearheading its own naval coalition in the area and has conducted retaliatory strikes on Huthi targets in Yemen, as has Britain.
The dozens of Huthi attacks have roiled shipping in the Red Sea, leading some companies to take alternative routes including a two-week detour around southern Africa.
On Monday evening, the Huthis said they had targeted three vessels in the previous 24 hours, including the British-registered Rubymar, the US-owned Sea Champion and the Navis Fortuna which they described as "American".
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