ISTANBUL — Turkey and Greece have reignited a decades-old disagreement over the sovereignty of a pair of uninhabited Aegean Islands, in a spat that analysts say risks aggravating other diplomatic disputes between the two countries.

The Greek defense minister, Panos Kammenos, flew over the two disputed islands on Wednesday, the Greek government said, in a pointed response to a visit three days earlier to nearby waters by the commander of the Turkish armed forces, Hulusi Akar.

The exchange is the most public disagreement over the tiny islands’ sovereignty since 1996, when soldiers from both countries landed on them before American-led mediation persuaded both sides to leave the area.

Turkey disputes Greece’s claim that the islands — known as Imia in Greece and Kardak in Turkey — entered Greek ownership in 1947, after first being assigned to Italy in 1923 following the fall of the Ottoman Empire.