The Etihad Airways flight, which landed in Israel on Tuesday, was the second airborne delivery of humanitarian cargo by the UAE that the Palestinians say they have turned down in a month.
"We refuse to receive it because it was coordinated directly between Israel and them (the UAE)," Palestinian civil affairs minister Hussein al-Sheikh told AFP.
"We were not part of the coordination."
Jordan and Egypt are the only Arab countries to hold official relations with Israel, but Gulf Arab nations like the UAE have been warming to the Jewish state recently amid shared concerns over Iran.
While a May 19 Etihad flight carrying Palestinian aid from Abu Dhabi to Tel Aviv was unmarked, Tuesday was the first time an Etihad aircraft landed in Israel bearing its logo, a source with knowledge of the flight told AFP.
The UAE's aid flights come as Israel prepares to move forward with annexing West Bank settlements and the Jordan Valley.
A peace plan announced by US President Donald Trump in January gave the green light for such annexations.
Analysts say Israeli Prime Minister Benjamin Netanyahu believes Arab states normalising ties with Israel will push the Palestinians to reach a peace deal.
But "there should be no normalisation before the end of the Israeli occupation," Al-Sheikh told AFP.
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