Transport ministry spokesman Ali Odaibat told the official Petra news agency Jordan had notified the International Civil Aviation Organisation about its concerns over the Israeli project and to "stress Jordan's keenness to protect its airspace".
Jordanian officials have repeatedly raised issue with the Timna airport, which is under construction just 10 kilometres from the Red Sea Jordanian resort town of Aqaba and King Hussein airport.
Officials have said it is too close and will affect takeoffs and landings at Aqaba's airport.
The new airport -- being built at a cost of more than USD 470 million -- would be located northeast of the Israeli resort town of Eilat, in the southern Aravah region of the Negev desert.