Husam Zomlot, the head of the Palestine Liberation Organization's office in Washington, would return to the Palestinian territories Wednesday, the statement said.
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It did not say how long Zomlot, the most senior Palestinian official in Washington, would be withdrawn for.
The Palestinians reacted furiously to President Donald Trump's December announcement recognising Jerusalem as Israel's capital and moving his country's embassy there from Tel Aviv.
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They consider the eastern part of Jerusalem their capital and countries have long kept their embassies in Tel Aviv, saying the future of the holy city was an issue to be negotiated between the Israelis and Palestinians.
The date of Monday's embassy opening also angered Palestinians, coming the day before they commemorate their mass displacement in the 1948 war surrounding the creation of Israel.
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The Israeli government welcomed the embassy move, which coincided with the anniversary of the country's independence.
The event was overshadowed by mass protests along the Gaza border in which Israeli fire killed 60 Palestinians.
The foreign ministry statement did not refer to the deaths, only the embassy move.
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