The airport is undergoing a 17 Million Euro expensive expansion plan at the moment with constructions being half way done. The expansion is crucial to enhance flight safety, especially during the peak operations period in summer. At the moment the operated ATR 72-600 by Sky Express cannot operate fully loaded on the 900m runway.
On 12 December 2009, an Olympic AirATR 42 (registration SX-BPA), performing flight OA6 from Athens to Naxos, was on a visual approach to runway 36 and had been handed off to Naxos Tower by air traffic control. The airplane was then seen in full landing configuration on final approach to Paros' runway 35 (length 710 meters/2300 feet) on the adjacent island. Paros Tower made contact on its frequency and Naxos Tower and ordered the aircraft to go around. The crew aborted the approach and subsequently landed safely in Naxos.[5]
On 12 July 2019, a Sky ExpressATR 42 (registration SX-FOR), about to perform flight GQ-405 from Naxos to Athens, was backtracking the runway for departure, when the aircraft went off the paved surface of the runway and came to a stop with the main gear in a ditch and the lower fuselage on the runway edge. There were no injuries, but the airport was closed for the rest of the day as a precautionary measure.[6][7]