Hundreds of Hamas fighters are stuck in tunnels in Israeli-controlled Gaza

A little over a week earlier, Israel and Hamas had agreed to a cease-fire. Israel responded to the deadly encounter with a round of airstrikes on Gaza that killed dozens of people.

The early test of the fragile truce pointed to a bigger problem: Hundreds of armed Hamas fighters are trapped in tunnels under the Israeli-controlled side of Gaza, and willing to take shots at Israel.

The situation is the result of Israeli efforts that began in May to flush out militants and destroy Hamas’s extensive tunnel system where the group has hidden fighters, hostages and weapons throughout the conflict. The strategy was to cut off sections of the underground web from one another. But Israel’s partial withdrawal under the U.S.-brokered cease-fire last month has left militants who remain behind the line trapped underground with no means of escape and dwindling supplies.

The fighters’ predicament and the possibility of further clashes posed by it constitute one of the biggest threats to the cease-fire. What to do with the besieged militants has become a sticking point in negotiations, Arab officials say. Hamas wants Israel to provide the fighters with safe passage into Hamas-controlled territory.

Israel wants them to surrender or to kill them.

“Israel’s policy in Gaza is clear: the IDF is acting to destroy the tunnels and eliminate Hamas terrorists without any restrictions within the yellow area under our control," Israel’s Defense Minister Israel Katz said in a post on X on Wednesday, referring to the Israeli military by its initials.

Washington wants to advance as quickly as possible to the next stage of the cease-fire, which envisages the deployment of an international stabilization force meant to secure Gaza, and the disarmament of Hamas. Both those aspects of the deal remain contentious.

Israeli and Arab officials estimate there are anywhere between 200 to 300 men underground. Hamas told mediators the number is closer to 100. Some may have already died from starvation, Arab officials say, as food supplies have dwindled. Most are struck in the southernmost city of Rafah, but some are also in parts of central and northern Gaza where Israel also maintains control, Israeli and Arab officials say, including neighborhoods east of Khan Younis, Beit Hanoun and Shuja’iyya.

In total, those fighters have killed three Israeli troops and injured several others, incidents that sparked waves of airstrikes that left over 145 Gazans dead, Palestinian health authorities said, without specifying how many were combatants.

Hamas has said it lost the ability to communicate with the men in March. The militant group said it didn’t order the attacks on Israeli troops. But on Sunday, as talks to free the militants advanced, Hamas said it found a way to communicate with them, according to the Arab officials.

Israeli military officials allege that Hamas has been able to communicate with the trapped fighters all along, as tunnels are equipped with communications systems. While the officials say they don’t believe Hamas ordered the attacks on troops, they say that Hamas had the option to order the men to stand down as Israeli troops approached their positions.

Hamas warned mediators before the cease-fire began that its trapped fighters might prefer to engage with Israeli troops rather than die of hunger or surrender, the Arab officials said.

Talks to free the trapped Hamas fighters began last week, after the U.S. broached the idea of offering them safe passage, Arab officials said. One proposal was to have them evacuated by the Red Cross. Israel initially agreed but wanted the fighters to give up their weapons and to tie their safe passage to the return of more dead hostages.

A U.S. official declined to comment on whether Washington broached the idea of safe passage for the trapped Hamas fighters but said talks are ongoing for decommissioning Hamas’s weapons and amnesty for its fighters once the group disarms.

On Tuesday, Israeli Prime Minister Benjamin Netanyahu switched Israel’s position and said the fighters wouldn’t be granted safe passage after an outcry by lawmakers from across the political spectrum who demanded militants involved with attacks on soldiers be either detained or killed.

“For several months, the Israeli military has been encircling and pursuing Hamas terrorists who are hiding in a ‘pocket’ in the Rafah area, terrorists who killed three of our heroic fighters just in the last few days," wrote Israel’s Finance Minister Bezalel Smotrich on Monday on X. “To let them leave safely a moment before Israeli fighters close in on them and eliminate them is a security and moral folly."

Israel fears that killing the trapped Hamas fighters could lead to Hamas halting the process of returning the deceased hostages remaining in Gaza, said Yaakov Amidror, a former national-security adviser under Netanyahu.

Because of that, as troops continue to search for the militants, they are seeking to capture the men rather than kill them, said Amir Avivi, a former senior Israeli defense official close to the security establishment.

“They are trying to map the underground area," said Avivi. “If they find exactly where they are they will need to surrender."

Hamas fighters have rarely surrendered throughout the two-year war, Israeli military officials have said.

The bodies of seven hostages remain in Gaza, and Israel alleges Hamas is dragging out the process to buy time to continue reconsolidating power in the enclave under the cover of a cease-fire and without any external forces deployed into the strip. The return of all the hostages remains the primary problem holding back the progression of the cease-fire deal to its next phase.

In the next phase of the cease-fire, the Trump administration hopes to begin supplying temporary housing for displaced Palestinians in areas of Gaza no longer under Hamas control, according to the U.S. official.

There are already hundreds to thousands of militiamen and their families who are opponents of Hamas living in the Israeli-controlled part of the strip, according to different estimates by Israeli military officials, Arab officials and senior commanders of the anti-Hamas militias.

But to attract more Gazans to areas outside of Hamas’s control, the U.S. and its Arab partners say the international stabilization force will first need to replace Israeli forces in those areas.

The establishment of that multinational force is itself facing complications due to disagreements over whether it should be involved with actively disarming Hamas or play a peacekeeping role.

Write to Dov Lieber at dov.lieber@wsj.com and Summer Said at summer.said@wsj.com