Guterres said nine UNRWA staff had already been dismissed for alleged involvement in Hamas's attack on Israel on 7 October and any UN employee involved in acts of terror would be held accountable, including through prosecution.
He said the UN Office of Internal Oversight Services, the highest investigative body in the UN system, had already been asked to mount an inquiry.
Israel's foreign ministry has vowed that UNRWA will play no role in Gaza when the conflict ends. The agency has 13,000 staff in Gaza and educates 30,000 children.
Israel formally handed information to the UNRWA commissioner general, Philippe Lazzarini, last Sunday alleging that up to 12 UNRWA staff had been involved in the 7 October attack.
Lazzarani immediately flew to New York to discuss the allegations with Guterres before informing key donors in the middle of the week and making an announcement on Friday, just as the international court of justice (ICJ) was delivering its verdict on South Africa's request for a provisional order directing Israel to allow aid into Gaza.
UN officials had hoped to prevent a donor collapse by being seen to act swiftly. But the US responded by suspending its funding, and since then nine other countries have followed suit, including the UK and Germany.
The US was the agency's largest bilateral donor in 2022, contributing more than $340m (£265m).
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