Instead of the historic site, Trump will be speaking at the Israel Museum in Jerusalem during his visit on May 22.The office of Israeli Prime Minister Benjamin Netanyahu declined to comment, referring any matters involving Trump's schedule to the US government.
Trump refused to visit the Masada National Park because "it was too hot" and he would have to travel using a cable vehicle - even though other presidents including Bill Clinton, George Bush and Barack Obama have travelled to the site in cable cars.
Helicopters are not allowed to land at the Masada fortress, which is a UNESCO World Heritage Site, due to the dust created by spinning propellers.
It is expected that Trump will replace the Masada trip with a speech at the Israel Museum on Monday.
In 1997, the wind blown by an Israeli military chopper that landed there damaged famed archaeological ruins, according to the Jerusalem Post. The fortress became a symbol of Jewish heroism after dozens of Jews there chose to kill themselves, 960 in total, rather than surrender to the Romans in 70 AD.
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Israeli media outlets reported that Trump had been scheduled to give his main speech on the Israeli leg of his upcoming trip overseas at the UNESCO World Heritage site.
Controversy rose earlier when American officials declined to allow Israeli leaders, including President Benjamin Netanyahu, to accompany Trump on the first visit of a sitting American president to the Western Wall, said The New York Times.
Masada, located on the Southern District of Israel, was mountain fortress constructed by King Herod. The Dead Sea Scrolls make an important setting'. The move angered Israel and officials asked the White House for an explanation.
Trump's stop in Israel is part of his first foreign trip as president, which includes visits to Saudi Arabia and the Vatican, as he visits the centers of three major world religions.
Since then, the only plane on Masada was a Cessna light aircraft that accidentally crashed into the site in 2006.