The device "was detected and tracked as part of routine procedures" and identified as "an unmanned aerial vehicle that had lost control", the ministry said in a statement.
Turkey dispatched F-16 fighter planes and "to prevent any adverse consequences, it was shot down in a safe area outside a populated area".
Turkey's President Recep Tayyip Erdogan warned on Saturday against the Black Sea becoming an "area of confrontation" between Russia and Ukraine, following several strikes in recent weeks on ships in the region.
A Turkish vessel was damaged on Friday in a Russian air strike near the Ukrainian port city of Odessa, just hours after Erdogan spoke with Russian President Vladimir Putin.
The Turkish leader earlier complained of a "worrying escalation" in the Black Sea, after attacks claimed by Ukraine on tankers linked to Russia off the Turkish coast.
Turkey, whose northern shore faces Ukraine and annexed Crimea, has maintained close ties with both Kyiv and Moscow since Russia's invasion of Ukraine in February 2022.
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