The midday attacks involved at least two drones that crossed from Iran into Azerbaijan's exclave of Nakhichevan, which borders Iran and is separated from mainland Azerbaijan by Armenia, said a foreign ministry statement.
"One drone fell on the terminal building of Nakhichevan Airport, while another drone fell near a school building in the village of Shekerabad," the ministry said, adding that the aircraft wounded two civilians and damaged the airport.
The defence ministry in Baku said it was "preparing the necessary retaliatory measures to protect the territorial integrity and sovereignty of our country and to ensure the safety of civilians and civilian infrastructure."
"These acts of attack will not go unanswered," it added.
Azerbaijan's foreign ministry said it had summoned the Iranian envoy in Baku to express "strong protest" over the attack, which "contradicts the norms and principles of international law and contributes to rising tensions in the region".
"Azerbaijan reserves the right to take appropriate retaliatory measures," it added.
Iran has long expressed concern that Israel -- a close ally of Azerbaijan and a key arms supplier -- could use Azerbaijani territory to stage attacks.
Last June, Azerbaijan reassured Iran that it would not allow its territory to be used for attacks against Tehran after Israel launched a large-scale strike on Iranian targets.
Tehran has historically been wary of separatist sentiment among its ethnic Azerbaijani minority, which makes up around 10 million of Iran's 83 million citizens.
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