Around 2.2 million Palestinian refugees are registered with UNRWA, the UN agency established in 1949 to support Palestinian refugees.
The vast majority have Jordanian citizenship.
Palestinian officials said Kushner pressured Jordan during a meeting in June "to strip its more than 2 million registered Palestinians of their refugee status so that UNRWA would no longer need to operate there," Foreign Policy reported.
In emails obtained by the US magazine, Kushner reportedly called for "an honest and sincere effort to disrupt UNRWA."
"This [agency] perpetuates a status quo, is corrupt, inefficient and doesn’t help peace," Kushner wrote.
"Our goal can't be to keep things stable and as they are. … Sometimes you have to strategically risk breaking things in order to get there."
UNRWA is a significant actor in the region, providing aid, education, and housing to five million Palestinian refugees in Jordan, Lebanon, Syria, the occupied West Bank and Gaza.
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While the US has funded the UN agency since it was formed in 1949, the Trump administration earlier this year cut $250 million from its budget.
US Ambassador Nikki Haley has said Washington will not restore the aid until the Palestinians agree "to come back to the negotiation table" with Israel.
Palestinian and US officials say the deliberate targeting of UNRWA is an attempt by the Trump administration to remove the issue of Palestinian refugees from the negotiating table.
Most Palestinian refugees were forcibly displaced during the establishment of the Israeli state in 1948, an event the Palestinians mark as the Nakba or the Catastrophe.
Another wave of Palestinians became refugees during the 1967 Arab-Israeli war and subsequent Israeli occupation of the West Bank, East Jerusalem and Gaza.
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