The UNRWA director, Philippe Lazzarini, called for a UN Security Council investigation into Israel's disregard for UN operations in Gaza following the deaths of 180 UNRWA staffers.
He also announced that the agency had raised $100 million in donations since the Israel-Hamas conflict began in October.
The comments came after an independent review found that Israel had not provided sufficient evidence to support claims that UNRWA staff were members of terrorist groups, but identified neutrality concerns, such as employees' social media posts.
UNRWA chief Matthias Schmidek's review found violations of neutrality in Gaza, East Jerusalem, and the West Bank.
Lazzarini, UNRWA's deputy commissioner-general, acknowledged the findings but expressed concern that attacks on UNRWA's neutrality aim to strip Palestinians of refugee status.
Established in 1949, UNRWA serves over 5.9 million Palestinian refugees and their descendants.
Lazzarini called for an independent investigation and accountability for the destruction of UN premises and the killing of 180 UNRWA staff and at least 400 civilians seeking UN protection during the conflict.
The UNRWA (United Nations Relief and Works Agency) premises in Gaza have been used for military purposes by both Israeli army and militant groups like Hamas, leading to arrests and torture of UNRWA staff.
An investigation is called for to ensure accountability and prevent lowering standards in future conflicts.
In January, allegations of UNRWA staff involvement in Hamas attacks resulted in donors freezing $450 million in funding for Gaza's 2.3 million residents in need.
While some countries have resumed donations, others, including the US, have not yet changed their funding status.
US National Security Council spokesman John Kirby stated that UNRWA funding remains suspended until there is real progress.
UNRWA, the United Nations agency for Palestine refugees, is currently operating on a hand-to-mouth basis, according to its commissioner-general, Filippo Grandi.
However, online fundraising for the agency has reached $100 million since October 7, indicating strong public support.
Israel has linked UNRWA to Hamas, the militant group responsible for an attack on October 7 that killed around 1,170 people, mostly civilians.
In response, Israel launched retaliatory bombardments and ground offensives, resulting in the deaths of at least 34,183 people in Gaza, mostly women and children.