The message was not getting through. Not through the phone calls or the emissaries or the public statements or the joint committee meetings. And so, frustrated that he was being ignored, President Joe Biden chose a more dramatic way of making himself clear to Israeli leaders. He stopped sending the bombs.

Biden’s decision to pause the delivery of 3,500 bombs to Israel was meant to convey a powerful signal that his patience has limits. While insisting that his support for the Jewish state remains “ironclad,” Biden for the first time since the Israel-Hamas war erupted last fall opted to use his power as Israel’s chief arms supplier to demonstrate his discontent.

The hold on the bombs represents a significant turning point in the 76-year-old relationship between the United States and Israel, historically one of the closest security partnerships in the world. But it may not necessarily be a breaking point. The Biden administration is still allowing most other weapons to be sent to Israel, and in fact officials emphasized that no final decision has been made on the bombs that are currently in limbo.

Biden hopes the selective pause will prompt Prime Minister Benjamin Netanyahu of Israel to forgo a long-threatened invasion of Rafah, the southern Gaza Strip city where more than 1 million Palestinians have taken refuge. The president has objected to such an operation out of fear that widespread civilian casualties could be caused by American bombs. He said Wednesday that he would also block the delivery of artillery shells that could be fired into the urban neighborhoods of Rafah.

“I’ve made it clear to Bibi and the war Cabinet, they’re not going to get our support if in fact they go on these population centers,” the president said in an interview with CNN’s Erin Burnett on Wednesday, referring to Netanyahu by his nickname. “We’re not walking away from Israel’s security; we’re walking away from Israel’s ability to wage war in those areas.”

He acknowledged in a way that he has rarely done that American bombs have killed innocent Palestinians. “Civilians have been killed in Gaza as a consequence of those bombs and other ways in which they go after population centers,” Biden said.

Israeli plans to storm Rafah have been a source of intense friction with the Biden administration for months. While the Americans oppose such an operation, the Israelis maintain they need to go into Rafah to finish destroying Hamas, which killed 1,200 people in its Oct. 7 terrorist attack on Israel.

The dispute has come to a head in recent days as Netanyahu and his war Cabinet appeared close to a decision to move against Rafah despite U.S. objections. Administration officials said they had begun reviewing arms last month that could be used in the operation and that Biden had signed off on the bomb hold last week.

“The decision means Biden has decided to use his only real form of leverage over Bibi — withholding weapons,” said Cliff Kupchan, chair of the Eurasia Group, who had just returned from a trip to the Middle East. “It’s a low point for U.S.-Israel relations, as it begins to put Israeli security in play. Biden had no choice. The war is a drag on his election campaign, on Democratic Party unity and on U.S. standing in the world.”

The administration was hoping the pause would send a quiet message and did not announce it publicly at first, but the Israelis leaked it. In the days since the decision, Israel ordered the evacuation of 110,000 civilians in Rafah, conducted airstrikes against targets on the edges of the city, sent in tanks and seized the crossing with Egypt. Although these moves were characterized as limited and not the beginning of the promised assault, they touched off alarms in the White House.

The Israeli actions, which came in part in response to Hamas rocket attacks that killed four Israeli soldiers last weekend, seem to be intended to keep the pressure on Hamas to agree to a temporary cease-fire in exchange for the release of some of the hostages taken Oct. 7.

Whether such a deal is possible remains uncertain. CIA Director William Burns, who has been deeply involved in the negotiations, met on Wednesday with Netanyahu in Jerusalem even as other officials conferred in Cairo about competing offers from the two sides. Reaching such a deal may be the only way to avoid a more serious rupture between Israel and the Biden administration, analysts said.

“What they’re asking for is for Israel not to go into Rafah in a significant way,” said Elliott Abrams, a Middle East specialist at the Council on Foreign Relations who served in multiple Republican administrations. “Barring a hostage deal, I think the Israelis are going to go into Rafah, and it is going to cause a great deal of tension.”

The relationship between the United States and Israel has been a singular one since the Jewish state declared its independence in 1948 and President Harry S. Truman just 11 minutes later made the United States the first nation in the world to recognize it. But the relationship has also long been marked by moments of deep stress.

At first, under both Truman and President Dwight D. Eisenhower, the United States refused to sell Israel weapons at all. President John F. Kennedy became the first to open up the arsenal by providing Hawk antiaircraft missiles. President Lyndon B. Johnson expanded ties by sending M-48 tanks, A-4 Skyhawk planes and F-4 Phantom planes.

Presidents have held back aid to Israel before to indicate displeasure or influence policy. President Ronald Reagan more than once delayed shipments of warplanes and other munitions out of dissatisfaction with Israeli intervention in Lebanon. President George H.W. Bush postponed $10 billion in housing loan guarantees to keep American money from being used to finance settlement construction in the West Bank.

Overall, since World War II, the United States has given more aid to Israel than any other country in the world. As of last year, the United States had provided $158.7 billion to Israel since its founding, the vast bulk of it, or $124.3 billion, for its military and its missile defenses, according to the Congressional Research Service. Under a 10-year memorandum of understanding sealed by President Barack Obama, Washington currently provides $3.8 billion a year in military aid, not counting the $15 billion in additional help approved last month by Congress and signed into law by Biden.

Republicans quickly criticized Biden on Wednesday after Defense Secretary Lloyd Austin publicly confirmed reports of the delayed bomb shipment at a Senate hearing. “This is obscene. It is absurd,” Sen. Lindsey Graham of South Carolina told the defense secretary. “Give Israel what they need to fight the war they can’t afford to lose.”

Sen. Mitch McConnell of Kentucky, the party’s leader in the Senate, said he had called Jake Sullivan, the president’s national security adviser, on Wednesday morning “to express my concern to the administration that the delay of shipment of weapons to Israel is just another way of trying to tell an ally how to conduct the war.” He and House Speaker Mike Johnson later sent a letter to Biden protesting the decision.

On the other hand, Democrats and progressives who have been pressing Biden to limit or cut off arms to curtail Israel’s war said the president’s action was long overdue and still not enough after more than 34,000 have died in Gaza, including both combatants and civilians.

Sen. Bernie Sanders, the democratic socialist from Vermont, said Biden’s decision was “absolutely right” but should only be the start. “Our leverage is clear,” he said. “Over the years, the United States has provided tens of billions of dollars in military aid to Israel. We can no longer be complicit in Netanyahu’s horrific war against the Palestinian people.”

The decision got the attention of Netanyahu and his war Cabinet. Shalom Lipner, a longtime adviser to multiple Israeli prime ministers, said it “struck a deep chord of concern within Israel, where people are wondering how limiting Israel’s access to weaponry — a move which is certain to embolden Hamas — might be reconciled with Biden’s oft-repeated ironclad commitment to its security.”

But he added that “it would be to Israel’s strategic detriment for the Netanyahu government to ignore the loud pushback from its main provider of military and diplomatic support.”

The 3,500 bombs held back last week include both 2,000-pound and 500-pound munitions.

The State Department is also still weighing whether to proceed with the delivery of Joint Direct Attack Munition guidance kits that can convert so-called dumb bombs into precision-guided weapons, but there is no imminent shipment at the moment. Moreover, officials said they would still provide “every dollar” of aid authorized in the new congressional package.

Kupchan said that the course of the U.S.-Israeli relationship would turn on what happens next. If Netanyahu defers to Biden’s judgment on Rafah, it may just be a momentary flare-up. But if the two leaders remain at a standoff, it could lead to a broader cutoff of weapons, which would have a more lasting effect.

“The foundation of U.S.-Israel relations is so strong that it won’t be significantly damaged by this move,” Kupchan said. “Further withholdings, however, while quite unlikely, would be a different story.”

The New York Times New Service