He assured the US remained “committed to facilitating a lasting peace agreement”.
Palestinians hurled stones and incendiary devices while the Israeli military used snipers, as black smoke poured from burning tires.
The Hamas-run health ministry said children were among those killed on May 14.
The mass demonstrations, led by Gaza’s Islamist rulers, Hamas, are part of a six-week protest dubbed the “Great March of Return”.
Israel’s army said 35,000 Palestinians were taking part in “violent riots” along the security fence and that its troops were operating “in accordance with standard procedures”.
It said it had killed three people trying to plant explosives near the security fence in Rafah.
Scores of Palestinians have been killed since the protests began. Thousands more have been wounded.
The US is moving its embassy from Tel Aviv to Jerusalem.
Top US officials will attend the opening ceremony of the new embassy, including President Trump’s daughter Ivanka and her husband, Jared Kushner.
The move is praised by Israel but condemned by Palestinians who are gathering for mass protests. Palestinians seek East Jerusalem as their own future capital, and see the US move as backing Israeli control over the whole city.
For its part, Israel considers all of Jerusalem as its indivisible capital.
Last year, President Donald Trump’s decision to recognize Jerusalem as Israel’s capital broke with decades of American neutrality on the issue, and put it at odds with most of the international community.
A small interim embassy will start operating on May 14 inside the existing US consulate building in Jerusalem.
A larger site will be found later when the rest of the embassy moves from Tel Aviv.
The opening ceremony was brought forward to coincide with the state of Israel’s 70th anniversary.
President Donald Trump is expected to address those attending May 14 event via video link.
Alongside senior White House advisers Ivanka Trump and Jared Kushner, Treasury Secretary Steven Mnuchin and Deputy Secretary of State John Sullivan will be at the ceremony.
The EU has voiced strong objections to the embassy move.
Israel’s PM Benjamin Netanyahu called on “all countries to join the US in moving their embassies to Jerusalem”.
Palestinian Authority President Mahmoud Abbas has described President Trump’s decision as the “slap of the century”.
Thousands of Palestinians are gathering for a protest along the perimeter fence that separates Israel and the Gaza Strip on May 14.
The timing of the embassy move has led to concerns about increased tension in Gaza.
Since the end of March, more than 40 Palestinians have been killed by Israeli soldiers in protests at the border.
UN human rights chief Zeid Ra’ad al-Hussein has accused Israel of using “excessive force”.
Israel maintains it has acted legitimately to protect its civilians from militants trying to breach the border.
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