Pierre Krahenbuhl lamented that the US decision to reduce funding for UNRWA this year by $300 million "has a political dimension that I think should be avoided.
"The United States suspended $65 million to the United Nations Relief and Work Agency (UNRWA) earlier this month, as well as a separate $45 million in food aid, AFP reported.
Thousands of teachers, medical professionals and other staff gathered in Gaza City on Monday to protest the cuts that UNRWA officials have warned could threaten the education of more than half a million children.
UNRWA is specifically dedicated to serving some 5.3 million registered Palestinian refugees in the West Bank, Gaza Strip, and throughout the Middle East.
Other refugees throughout the world receive aid through the UN Refugee Agency under the auspices of the UN High Commissioner for Refugees.
Israel has often criticized UNRWA, accusing it of perpetuating the plight of Palestinians by allowing the descendants of first-generation Palestinian refugees -- those who fled what is today Israel when it was declared an independent state in 1948 -- to maintain refugee status in their host countries.
Netanyahu has called for UNRWA to be shut down altogether.
The US relationship with the Palestinians has been terse since Trump’s declaration recognizing Jerusalem (al-Quds) as the capital of Israel and vow to relocate the US embassy there. The move sparked a new wave of unrest between Israel and the Palestinians, and called into question the US role in future peace talks.
The status of al-Quds is among the most contentious in the Israeli-Palestinian conflict. Israel claims all of Jerusalem (al-Quds) as its united capital, while the Palestinians see the eastern sector as the capital of their future state.