UNRWA Commissioner-General Pierre Krahenbuhl speaks during a news conference at a UN-run school in Gaza City in January 2018. Photo: Reuters / Suhaib Salem.

The head of a UN agency that aids Palestinian refugees resigned on Wednesday, the United Nations said, amid an investigation into misconduct allegations.

Commissioner-General Pierre Krahenbuhl was replaced earlier on Wednesday until a review of “management-related matters” at the agency was completed, the UN Relief and Works Agency for Palestine Refugees (UNRWA) said in a statement.

Krahenbuhl then informed UN Secretary-General Antonio Guterres that he was resigning, effective immediately, UN spokesman Stephane Dujarric told reporters in New York.

“At this time, it is vital that member states and other partners remain committed to UNRWA and the services it provides,” Dujarric said.

UNRWA aids more than 5 million registered refugees in the West Bank, Gaza Strip and East Jerusalem, as well as in Jordan, Lebanon and Syria.

Guterres had earlier on Wednesday appointed Christian Saunders, the agency’s acting deputy commissioner general, as officer-in-charge for the interim period.

Krahenbuhl was notified in March that an investigation was underway by the UN Secretariat in New York “based on allegations received against UNRWA personnel relating to unsatisfactory conduct,” an UNRWA spokeswoman said.

Krahenbuhl, a Swiss national, took over the UNRWA post in 2014. He was previously director of operations at the International Committee of the Red Cross.

Dujarric said in a statement on Wednesday that the preliminary findings of the investigation by the UN Office of Internal Oversight Services “exclude fraud or misappropriation of operational funds” by Krahenbuhl.

“There are, however, managerial issues that need to be addressed,” he said.

UNRWA has faced budgetary difficulties since last year, when the United States, its biggest donor, halted its aid of $360 million per year. The United States and Israel have both accused UNRWA of mismanagement and anti-Israeli incitement.

Switzerland, the Netherlands and Belgium have separately suspended payments to UNRWA over the management issues that are now under investigation. The agency’s spokeswoman says it still needs $89 million to keep operating until the end of this year.

“It is critical for the international community to support the crucial work performed by the agency in the areas of health, education, and humanitarian assistance, which is a source of stability in a volatile region,” Dujarric said.