It said one drone fell on an airport in Nakhchivan and another landed near a school.
In a statement, it condemns the attacks, demands an explanation from Iran, and says it reserves the right to take “appropriate response.”
There has been no immediate comment from Iran.
Reports say missiles struck Nakhchivan International Airport in Azerbaijan on Thursday, as the war between Iran, Israel and the United States appeared to spread beyond the Middle East.
Local media and witnesses reports on social media show several explosions around the airport in Nakhchivan, an Azerbaijani exclave bordering Iran, Turkey and Armenia.
Video circulating online showed fire engines and paramedics at the scene, with smoke rising near parts of the airfield.
Authorities in Azerbaijan have not yet confirmed the extent of damage or whether there were casualties.
The attack would be unusual as Azerbaijan does not host U.S. military bases, despite maintaining close political and security ties with both Israel and the United States.
Nakhchivan occupies a strategically sensitive position on Iran’s northern border. The region lies close to Turkey, which maintains close military ties with Azerbaijan.
The reported strike comes as fighting between Iran and Israel entered its sixth day, following joint U.S.–Israeli attacks on Iranian targets launched over the weekend.
Iran has responded with waves of missile and drone attacks against Israel and against U.S. bases across the Middle East, while Israel has continued air strikes on Iranian military infrastructure and on Hezbollah targets in Lebanon.
The conflict has already spread across multiple countries in the region, with incidents reported in Lebanon, Iraq, Kuwait, Saudi Arabia and the Gulf states.
It was not immediately clear whether the reported incident in Nakhchivan was a direct strike, a missile that went off course, or debris from an intercepted projectile.
Officials in Iran have not commented on the reports.
If confirmed, the strike would represent one of the first impacts of the conflict in the South Caucasus, raising concerns that the fighting could expand beyond the Middle East.
