Philippe Lazzarini, the head of UNWRA, said in a post on the social media platform X on Thursday that he had decided to close the compound until proper security was restored. He said Thursday's incident was the second in less than a week, Daily Sabah English website in Turkey reported.
"This is an outrageous development. Once again, the lives of UN staff were at a serious risk," he said.
"It is the responsibility of the State of Israel as an occupying power to ensure that United Nations personnel and facilities are protected at all times," he said.
UNRWA, set up to deal with the Palestinian refugees who fled or were forced from their homes during the 1948 war around the time of Israel's creation, has long been a target of Israeli hostility.
Since the start of the war with Gaza Israeli officials have called repeatedly for the agency to be shut down, accusing it of complicity with the Palestinian resistance movement Hamas in Gaza, a charge the United Nations strongly rejects.
Israel considers all of Quds its indivisible capital, including eastern parts it captured in a 1967 war, which Palestinians seek as the future capital of an independent state.
Lazzarini said staff were present at the time of the incident but there were no casualties. However, outdoor areas were damaged by the blaze, which was put out by staff after emergency services took time to respond.
There was no immediate comment from the Israeli police.
Lazzarini said groups of Israelis had been staging regular demonstrations outside the UNRWA compound for the past two months and said stones were thrown at staff and buildings in the compound this week.
In footage shared with Lazzarini's post, smoke can be seen rising near buildings at the edge of the compound while the sound of chanting and singing can be heard.
A crowd accompanied by armed men were seen outside the compound chanting "Burn down the United Nations," Lazzarini said.
MNA