The Tánaiste has accused Israel of launching a misinformation campaign against UNRWA.
Micheál Martin met with the Commissioner-General of the UN agency which helps Palestinian refugees, Philippe Lazzarini, in Dublin earlier.
Irish funding for the agency of €20 million was also announced.
A number of countries have paused funding the agency after Israeli allegations that staff members were involved in the Hamas attacks on October 7th.
The Tánaiste said he is "deeply concerned" that a number of key donors suspended their funding based on allegations "against a very small number of staff that have yet to be proven".
Mr Lazzarini said if those countries do not reinstate funding, the agency will face financial issues from March onwards.
Mr Martin said he believes Israel is trying to undermine the agency's work.
"I think almost from the beginning of the war Israel has been undermining UN agencies more generally and the United NAtions itself, and specifically UNRWA," he said.
"I think it's part of a wider position around the right of return of refugees, in the context of the establishment of a Palestinian state, if we were to arrive at a two-state solution."
UNRWA Commissioner General Philippe Lazzarini meets with Taoiseach Leo Varadkar in Dublin, 15-2-24. Image: @UNLazzarini/XMr Lazzarini said there are already significant challenges ahead of any potential Israeli military operation in Rafah.
"It's becoming more and more difficult to operate in Rafah itself," he said.
"Yesterday for the first time the UN could not operate with a minimum of protection, which was the local police.
"And because we had no local police our trucks and conveys at the border have been looted and vandalised by hundreds of young people," he added.
UNRWA has seen more than 150 of its staff have killed during Israeli bombardment of the Gaza Strip.
Human rights obligations
Yesterday Taoiseach Leo Varadkar urged the European Union to urgently "review whether Israel is complying with its human rights obligations".
In a letter to the European Commission President, Leo Varadkar and Spanish Prime Minister Pedro Sanchez said the expanded Israeli military operation in the Rafah area of Gaza poses a "grave and imminent threat that the international community must urgently confront".
The two leaders noted that Israel has a right to defend itself but insist that its actions "must be in line with international law and International Humanitarian Law, including in the obligation to protect civilians".
They also called on the Commission to propose measures that can be taken by the EU if Israel is found to be in breach of its human rights obligations.
