Trump had originally meant to give his keynote speech at Masada but the visit was cancelled.
The president refused to land his helicopter at the base of the historic site and take a cable auto up as former Presidents Bill Clinton and George W. Bush had done, Newsweek reported, citing Israel's Channel 2.
Helicopters were once allowed to land on the monument, but the rules were changed in the 1990s, because dust clouds stirred up by helicopter landings damaged the fortress and artifacts, the Jerusalem Post reported.
In 1997, an Israeli Air Force helicopter landed in the middle of Masada, one of Israel's most ancient and famous archaeological parks.
Trump's visit to Israel has already been under a diplomatic test.
'Well Masada was too hot, so we found a great spot instead for POTUS, ' Eitan Weiss, deputy spokesperson for the Israeli Foreign Ministry tweeted, seemingly mocking the president, according to Newsweek report. White House officials also told Israelis that they didn't want Netanyahu to accompany Trump during his visit to the Western Wall as it was in the West Bank.
Comedian John Oliver, host of the HBO show "Last Week Tonight"
Donald Trump (l.) said he planned on firing James Comey (r.) regardless of what his staff recommended. If you said he fired Comey because he's investigating Russian Federation , I'd believe you .
King Herod is believed to have built the fortress, but its defining story is that its Jewish rebel defenders who-under threat from a Roman siege-killed themselves rather than be captured alive by the invading forces sometime between 73 and 74 AD.
The former president and Netanyahu had a fraught relationship during his term because of stalled Israeli-Palestinian peace talks.
This announcement left Netanyahu's angry and White House officials had to reiterate that this was not Trump's position.
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.
Masada is a UNESCO World Heritage Site that sits upon a mountain in the Judean Desert.
The Masada is one of Israel's most important historic sites.