US officials have signalled to Israel that more arms shipments could be delayed if the Israeli military pushes ahead with an offensive in Rafah, Gaza, in what would mark the start of a major pivot in relations between the two countries. Lloyd Austin, the US defence secretary, confirmed on Wednesday that the Biden administration had paused the supply of thousands of large bombs to Israel, in opposition to apparent moves by the Israelis to invade the city. “We’ve been very clear … from the very beginning that Israel shouldn’t launch a major attack into Rafah without accounting for and protecting the civilians that are in that battle space,” Austin told a Senate hearing. “And again, as we have assessed the situation, we have paused one shipment of high payload munitions,” he said, adding: “We’ve not made a final determination on how to proceed with that shipment.” Gilad Erdan, Israel’s ambassador to the UN, said he did not believe the US would stop supplying arms to Israel, but called Washington’s decision to hold up some weapons shipments “very disappointing”, even frustrating. Joe Biden “can’t say he is our partner in the goal to destroy Hamas while on the other hand delay the means meant to destroy Hamas”, Erdan told Israel’s Channel 12 News. The hold on the munitions delivery also drew a quick response from the Republican leadership. “Israel faces an existential and multi-front threat … and daylight between the United States and Israel at this dangerous time risks emboldening Israel’s enemies and undermining the trust that other allies and partners have in the United States,” the House speaker, Mike Johnson, and Senate Republican leader, Mitch McConnell, wrote in a letter to the president. The White House decision drew support from progressive Democrats, including Senator Chris Van Hollen. “We should use the tools available to us to enforce the president’s objectives and US policy,” Van Hollen said. “A partnership must be a two-way street, not a one-way blank cheque.” US officials made clear that the pause would not be a one-off if the Rafah offensive went ahead: other arms deliveries that have already been approved could be delayed, and shipments waiting for approval could also face obstacles, such as a pending consignment of 6,500 joint direct attack munitions, or JDAMs, which convert freefall “dumb bombs” into precision-guided weapons. A Guardian investigation this week found a US-made JDAM was used in a March airstrike in southern Lebanon that killed seven health workers. Analysis of debris found at the site of the attack revealed shrapnel from a 500lb (227kg) Israeli MPR bomb, as well as the parts of the JDAM that connect the munition to the guidance system and remnants of its motor. The US administration has refused to use the phrase “red line” but has stressed that Biden was serious when he told Benjamin Netanyahu in a call on 4 April that an attack on Rafah would lead to a significant re-evaluation of the relationship. The weapons – 1,800 2,000lb bombs and 1,700 500lb bombs – had long been seen by experts as the most likely to be targeted for any potential restrictions on arms supplies to Israel given how destructive they are in urban settings. US officials insist that the pause is not because of legal concerns, but is a policy decision. There is nervousness in the administration about making legal judgments in case they are used against Israel in legal disputes before the international criminal court and the international court of justice. However, the Guardian understands that conversations in recent months have focused on how the Israeli military’s use of certain munitions diverges from the Pentagon’s rules on the use of such weapons in heavily populated urban settings. Israeli troops on Tuesday took control of the Palestinian side of the Rafah crossing between Gaza and Egypt, a vital lifeline that is now closed. Israeli officials said it was the first step towards a full-scale assault on Rafah city, an offensive Biden has been trying to head off. Rafah’s mayor, Ahmed al-Sofi, warned that the southern city was “on the brink of a humanitarian catastrophe of unprecedented proportions” in an appeal to the international community on Wednesday. “The streets of the city echo with the cries of innocent lives lost, families torn apart, and homes reduced to rubble,” he said. The highly significant US move on arms supplies comes amid mounting international pressure on Israel to pull back from a full-scale attack after its seizure on Tuesday of Rafah’s border crossing with Egypt, and criticism of Israel’s use of large aerial munitions in areas packed with civilians. Austin’s comments confirmed earlier briefings by unnamed officials that the weapons shipment had been held up because of Israel’s threat of a full-scale offensive in Rafah. ”We are especially focused on the end use of the 2,000lb bombs and the impact they could have in dense urban settings as we have seen in other parts of Gaza. We have not made a final determination on how to proceed with this shipment,” one US official said. A second US official, also speaking anonymously and quoted by the Washington Post, said the decision was a “shot across the bow” intended to convey to Israel the seriousness of US concerns about the Israeli offensive in Rafah. An Israeli military spokesperson attempted to play down the shipment delay – saying that allies resolve any disagreements “behind closed doors”. However, the move appeared to mark a significant moment in US policy. While the US, EU, UK and other countries have pursued an escalating sanctions campaign against extremist Israeli settlers and far-right organisations, against the background of the Gaza war and settler violence on the West Bank, US attention has moved recently to the Israel Defense Forces. The weapons hold-up comes against the background of the expected delivery of a report by the US Department of State that examines whether Israel’s war conduct is credibly in compliance with assurances that American-supplied weapons will not be used in contravention of US and international humanitarian law. The White House and Pentagon declined to comment. Israeli forces on Tuesday seized the main border crossing between Gaza and Egypt in Rafah, cutting off a vital route for aid into the Palestinian territory. On Monday, the Israeli army had called on 100,000 people in eastern Rafah to evacuate. Despite the assault in Rafah, the US has said it believes a revised Hamas ceasefire proposal may lead to a breakthrough as talks resume in Cairo. Israel had previously said the terms in the proposal had been softened, but the White House spokesperson John Kirby said the new text suggested the remaining gaps could “absolutely be closed”. The CIA director, William Burns, is to travel to Israel on Wednesday to meet Netanyahu, a source said. The delays to US arms shipments appeared to be the first since the Biden administration offered its full support to Israel after Hamas launched its 7 October attack, in which about 1,200 people were killed and about 250 others were abducted, of whom 133 are believed to still be in captivity in Gaza, according to Israeli tallies. Israel’s campaign to destroy Hamas has led to a seven-month military campaign that has killed 34,789 Palestinians, most of them civilians, the Gaza health ministry has said.