Israel has taken measures in recent months to ensure that air traffic into the Red Sea town, wedged between Jordan and Egypt, could not be targeted by Islamist militants in Egypt's Sinai Peninsula.
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Those steps have included occasional rerouting of daytime flights so they do not skirt the Egyptian frontier – patterns that aviation experts said forced planes to make steep turns.
El Al, which has three daily daytime flights to Eilat from Tel Aviv's Ben-Gurion Airport, said new landing and takeoff patterns for the resort town that were put in place on Monday did not meet international aviation safety standards.
"The chief executive of El Al expressed a deep concern to the director of the Civil Aviation Authority about the implications of the new directive in terms of safety," the company said, without further explaining why it believed the new flight paths were unsafe.
"El Al expects the aviation authorities to urgently deal with the matter to allow the safe and regular operation of flights to Eilat," it said.
Eilat airport (Photo: Meir Ohayon)
Israel's Transportation Ministry that oversees civil aviation had no immediate comment.
Last month, Israel shut down the Eilat airport for a couple of hours citing security concerns.
It has also boosted rocket defenses near its southern border to counter possible attacks from Sinai, where Egypt's army has been cracking down on militant groups.
El Al's nighttime flights, whose routing has not been changed, are unaffected. Other Israeli airlines, which fly smaller aircraft to Eilat, announced no changes to their schedules.