At a Security Council meeting, Guterres called for a humanitarian ceasefire on Tuesday amid the deepening crisis in Gaza, and told the Security Council that "clear violations of international humanitarian law" were being witnessed.
He called Hamas' October 7 murder and kidnap rampage "appalling," and said "nothing can justify the deliberate killing, injuring and kidnapping of civilians, or the launching of rockets against civilian targets".
"It is important to also recognise the attacks by Hamas did not happen in a vacuum," Guterres said.
"The Palestinian people have been subjected to 56 years of suffocating occupation. They have seen their land steadily devoured by settlements and plagued by violence; their economy stifled; their people displaced and their homes demolished."
"But the grievances of the Palestinian people cannot justify the appalling attacks by Hamas. And those appalling attacks cannot justify the collective punishment of the Palestinian people. Excellencies, even war has rules," he added.
His comments angered Israeli Foreign Minister Eli Cohen, who was in the chamber as Guterres spoke.
"In what world do you live?" said Cohen. "Definitely, this is not our world."
Writing on social media later, Cohen said that "after the October 7th massacre, there is no place for a balanced approach. Hamas must be erased off the face of the planet!"
Israel's ambassador to the United Nations, Gilad Erdan, called on Guterres to resign, saying he had "expressed an understanding for terrorism and murder."
Then, on Wednesday, Erdan said his country would block visas for United Nations officials. It had already rejected an application by the UN Under-Secretary-General for Humanitarian Affairs and Emergency Relief Co-ordinator Martin Griffiths, Erdan told the Israeli Army Radio channel.
"It's time we teach them a lesson," added Erdan.
The deepening spat exposes tensions around the calls from some international observers for a ceasefire, amid a worsening humanitarian crisis in Gaza.
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In an effort to "set the record straight," Guterres said Wednesday he was "shocked by misinterpretations by some of my statement yesterday in the Security Council – as if I was was justifying acts of terror by Hamas."
"This is false. It was the opposite," he told reporters, restating his condemnation of the October 7 attacks.
But Guterres did not back away from his Tuesday call for a ceasefire, or from his nod towards the historical treatment of Palestinians.
The main United Nations agency working in Gaza said it would be forced to halt its operations by Wednesday evening due to a lack of fuel, with the territory having faced days of airstrikes and near-total blockade following the Hamas attacks.
Efforts in the UN to endorse a ceasefire have so far been scuppered, with the US vetoing a draft resolution raised by Brazil last week.
Secretary of State Antony Blinken on Tuesday told the agency that "humanitarian pauses must be considered" to allow aid to reach civilians in Gaza, though he notably avoided the phrase "ceasefire."
On Monday, National Security Council spokesman John Kirby rebutted calls for a ceasefire, telling CNN that Hamas must first release hostages held in Gaza.
The World Health Organisation meanwhile reiterated calls on Tuesday for a ceasefire, saying it is "unable to distribute fuel and essential, life-saving health supplies to major hospitals in northern Gaza due to lack of security guarantees."
Six hospitals in Gaza have been forced to shut due to a lack of fuel, WHO added.