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In a country where military service is compulsory for most Jewish Israelis, both men and women, the exemption for the ultra-Orthodox has long prompted resentment. But anger over the group’s special treatment has grown as the war in Gaza has stretched into its ninth month, requiring tens of thousands of reservists to serve multiple tours and costing the lives of hundreds of soldiers.

“These days, in the midst of a difficult war, the burden of that inequality is more acute than ever — and requires the advancement of a sustainable solution to this issue,” the Supreme Court said in its ruling.

The decision threatened to widen one of the most painful divisions in Israeli society, pitting secular Jews against the ultra-Orthodox, who say their religious study is as essential and protective as the military. It also exposed the fault lines in Mr. Netanyahu’s coalition, which depends on the support of two ultra-Orthodox parties that oppose their constituents’ conscription, even as other Israelis are killed and wounded in Gaza.

Israeli courts have ruled against the exemption before, including Supreme Court decisions in 1998, 2012 and 2017. The top court has repeatedly warned the government that to continue the policy, it must be written into law — though that law would be subject to constitutional challenges, as previous ones were — while also giving the government time to hammer out legislation.

But for seven years, since the last law was struck down, successive Israeli governments have dragged their feet in drafting new legislation. In 2023, the law finally reached its expiration date, leading the Israeli government to order the military simply not to draft the ultra-Orthodox while lawmakers worked on an exemption.

On Tuesday, the court indicated that its patience had finally run out, striking down that order as illegal. It did not set a timeline for when the military must start conscripting tens of thousands of draft-age religious students. Such a move would likely prove a massive logistical and political challenge, as well as be met with mass resistance by the ultra-Orthodox community.

Gali Baharav-Miara, Israel’s attorney general, in a letter to government officials on Tuesday, said the military had committed to draft at least 3,000 ultra-Orthodox religious students — out of more than 60,000 of draft age — during the coming year. She noted that the number would come nowhere near to bridging the gap in military service between the ultra-Orthodox community and other Israeli Jews.

Instead, the ruling included a means of pressuring the ultra-Orthodox to accept the court’s judgment: the suspension of millions of dollars in government subsidies given to religious schools, or yeshivas, that previously supported the exempted students, striking a blow to revered institutions at the heart of the ultra-Orthodox community.

The court’s ruling threatens Mr. Netanyahu’s fragile wartime coalition, which includes secular members who oppose the exemption and ultra-Orthodox parties that support it. Either group breaking ranks could cause the government to collapse and call new elections, at a time when popular support for the government is at a low. The opposition in the Israeli Parliament largely wants to end the exemption.

The Hamas-led attacks on Oct. 7 — which ignited the eight-month war in Gaza — somewhat loosened the ultra-Orthodox stance on the draft, with some leaders saying that those who could not study scripture should go to the military.

“Still, the maximum that the ultra-Orthodox community is willing to give is far less than what the general Israeli public is willing to accept,” said Israel Cohen, a commentator for Kol Barama, an ultra-Orthodox radio station.

But the ultra-Orthodox parties, with few palatable options, might not be eager to bring down Mr. Netanyahu’s coalition, he said. “They don’t see an alternative, so they’ll try to make it work for as long as they can,” said Mr. Cohen. “They will compromise more than they might have been willing to a year ago in an attempt to preserve the government.”

For now, the military must devise a plan to potentially welcome to its ranks thousands of soldiers who are opposed to serving and whose insularity and traditions are at odds with a modern fighting force.

The court’s decision creates a “gaping political wound in the heart of the coalition” that Mr. Netanyahu now must urgently address, said Yohanan Plesner, chairman of the Israel Democracy Institute, a Jerusalem-based think tank.

In a statement, Mr. Netanyahu’s Likud party criticized the Supreme Court for issuing a ruling when the government was planning to pass legislation that would render the case obsolete. The government’s proposed law, the party said, would increase the number of ultra-Orthodox conscripts while recognizing the importance of religious study.

It was unclear whether Mr. Netanyahu’s proposal would ultimately hold up to judicial scrutiny. But if passed by Parliament, a new law could face years of court challenges, buying the government additional time, said Mr. Plesner.

The Supreme Court’s decision on Tuesday immediately sparked outrage among ultra-Orthodox politicians. Many ultra-Orthodox view military service as a gateway to assimilation into a secular Israeli society that would lead young people to deviate from a lifestyle guided by the Torah, the Jewish scriptures.

“The State of Israel was established in order to be a home for the Jewish people, for whom Torah is the bedrock of their existence. The Holy Torah will prevail,” Yitzhak Goldknopf, an ultra-Orthodox government minister, said in a statement on Monday.

After the Oct. 7 Hamas-led attack on southern Israel, Israelis united in determination to strike back. But as thousands of reserve soldiers were asked to serve second and third tours in Gaza, the fault lines in Israeli society quickly resurfaced.

Some Israeli analysts warn that war could spread to additional fronts in the West Bank and the northern border with Lebanon, leading the government to call for more conscripts and further straining relations between secular and ultra-Orthodox Jews.

Already many Israelis — secular, religious and ultra-Orthodox alike — see the draft issue as just one skirmish in a broader cultural battle over the country’s increasingly uncertain future.

Ultra-Orthodox Jews have been exempt from military service since the founding of Israel in 1948, when the country’s leadership promised them autonomy in exchange for their support in creating a largely secular state. At the time, there were only a few hundred yeshiva students.

The ultra-Orthodox have grown to more than a million people, roughly 13 percent of Israel’s population. They wield considerable political clout and their elected leaders became kingmakers, featuring in most Israeli coalition governments.

But as ultra-Orthodox power grew, so did anger over their failure to join the military and their relatively small contribution to the economy. In 2019, Avigdor Lieberman, a former ally of Mr. Netanyahu, rebuffed his offer to join a coalition that would legislate the draft exemption for the ultra-Orthodox. The decision helped send Israel to repeated elections — five in four years.

Last year, after Mr. Netanyahu returned to power at the helm of his current coalition, he sought to legislate a plan to weaken the country’s judiciary, setting off mass protests. For the ultra-Orthodox, who backed the judicial overhaul, a major motivation was ensuring that the Supreme Court could no longer impede their ability to avoid the draft.

Ron Scherf, a lieutenant colonel in the Israeli reserves, said many soldiers were frustrated to be serving multiple tours of duty during the war, even as ultra-Orthodox Israelis are “never called up in the first place.”

An activist with Brothers in Arms, a collection of reserve soldiers who oppose Mr. Netanyahu, Mr. Scherf asked, “How can Israel just allow an entire community to be exempt from its civic duties?”

Gabby Sobelman, Johnatan Reiss and Myra Noveck contributed reporting.