GOLAN HEIGHTS — Quietly, over the last year, hundreds of sick Syrian children and their chaperones have been whisked across enemy lines at dawn for treatment at clinics in Israel, slipping back home after dark.
Truckloads of supplies have passed into Syrian villages through a gate in the sturdy security fence that Israel has constructed since Syria erupted into civil war, including stacks of flour, generators, half a million liters of fuel, construction materials, tons of shoes, baby formula, antibiotics and even a few vehicles and mules.
This week, the Israeli military revealed the scope of the humanitarian aid project, which it calls Operation Good Neighbor and which began in June 2016 along the Israeli-Syrian boundary on the Golan Heights.
The aid project depends on an extraordinary level of cooperation between old foes on both sides of the decades-old armistice lines separating the Syrians and Israelis. Military officials say they coordinate directly with Syrian doctors and village leaders to gauge needs.
The humanitarian effort is likely to burnish the reputation of the Israeli military, which is usually viewed as an occupying force and formidable war machine. It also yields immediate security benefits by giving Syrian border villages — dominated by rebel forces fighting the government of President Bashar al-Assad — an interest in keeping out more radical anti-Israeli militias, and represents what officials say is a longer-term investment in stabilizing the area.
“The aid creates a positive awareness of Israel on the Syrian side,” said Col. Barak Hiram, the commanding officer of Israel’s 474 Golan Brigade, adding that it could lay the “first seeds” of some form of future agreement.
Most of the supplies are donated by Israeli and foreign nongovernmental organizations, while the Israeli government has footed the bill for medical treatment. According to the Multifaith Alliance for Syrian Refugees, a New York-based network of organizations involved in the aid effort, Israel has also become an efficient, if unlikely, staging area for Syrian aid groups operating abroad that, facilitated by the Israeli military, are now shipping goods into Syria through Israeli ports.
The extent of the project became known days after the United States and Russia announced a cease-fire agreement for southern Syria, territory that includes the areas covered by Operation Good Neighbor, and after President Trump’s cancellation of the clandestine and failing American program to provide arms and supplies to Syrian rebel groups.
Prime Minister Benjamin Netanyahu, speaking to Israeli reporters during a trip to Europe this week, said he was utterly opposed to the cease-fire deal because of concerns that it would allow Shiite militias backed by Israel’s archenemy, Iran, to dig in close to its borders.
“Netanyahu is upset because the Jordanians were told that the Shiite militias would be kept 40 kilometers from their border,” said Ehud Yaari, an Israeli analyst and fellow of the Washington Institute for Near East Policy. “Israel did not get the same promise. We were left out.”
But discussions about the cease-fire are continuing, Mr. Yaari said, and the Israeli protests seemed aimed at trying to shape the outcome.
Israel says it maintains a policy of nonintervention in Syria’s civil war, which began in 2011. But it has frequently bombed convoys and stores of weapons destined for Hezbollah, the Iranian-backed Lebanese militia fighting in Syria on behalf of Mr. Assad. On other occasions, it has retaliated against Syrian government positions for the spillover of errant fire into the Israeli-controlled Golan Heights.
According to Israeli military officials, extremist groups associated with the Islamic State control about 20 percent of the territory along the Syrian side of the Golan boundary, concentrated in the south. A mélange of other Sunni rebel groups, including affiliates of Al Qaeda, control an additional 65 percent, while the Syrian Army, Shiite allies and Druze loyalists control about 15 percent in the north.
Israeli analysts say it can be assumed that cash, ammunition and intelligence assets also pass through the fence on the Golan Heights, the strategic plateau that Israel captured from Syria in the 1967 war. A recent Wall Street Journal article quoted local Syrian rebels saying that they regularly received cash for salaries and weapons as part of the Israeli effort to push hostile forces from the border villages. Israel has not explicitly denied the report, and the military would not comment.
But Israeli military officials insist that Operation Good Neighbor deals purely with humanitarian aid and that they would not jeopardize the emerging climate of cooperation or taint it by mixing in weapons transfers and intelligence gathering.
Since Israel and Syria are technically in a state of war and have no diplomatic relations, Israel has not taken in masses of Syrian refugees as other countries have done. Even a government proposal to bring in 100 orphaned Syrian children was dropped.
Still, many Israelis have expressed distress over standing by as the humanitarian disaster has unfolded in Syria, which is what motivated the military to undertake the operation, officials said.
Syrians wounded in the fighting first arrived at the Israeli border fence early in 2013, desperate for help.
“We faced a dilemma,” said Dr. Noam Fink, the chief medical officer of the Israeli military’s northern command. “The decision was made by our commanders and our government to allow them to enter the country and to give them full medical treatment.”
Since then, with medical facilities in war-ravaged towns and villages barely functioning, Israel has treated about 4,000 war-wounded or sick Syrians.
Israel says it is now getting aid to an area inhabited by about 200,000 Syrians, including around 400 displaced families living in tent encampments along the international boundary, and is helping equip new clinics in the area.
“So far the strategy is working,” said Amos Harel, the military affairs analyst for the newspaper Haaretz, noting the relative quiet along the Israeli-Syrian cease-fire line. “It is an intelligent policy. It is not only altruistic.”
Georgette Bennett, who founded the Multifaith Alliance in 2013, said her network had the ability to reach deeper on the Syrian side, covering an area of 1.5 million Syrians. The cooperation between Israelis and Syrians is “a great glimmer of hope coming out of this tragedy,” said Ms. Bennett, a Hungarian-born former refugee and the daughter of Holocaust survivors.
The alliance’s director of humanitarian relief and regional relations, Shadi Martini, is a Syrian who said he managed a hospital in Aleppo, a city that has been an epicenter of the war, before fleeing the country in 2012. When he first heard about the Israelis’ aid, he said: “It was a very big shock to me. Syrians were brought up to fear Israelis as the devil who wants to kill us and take our land.”
Speaking by telephone from Michigan, where he now lives, Mr. Martini said he had since visited Israel five times to push for, and coordinate, the effort with the Israeli military. “It has struck a chord with a lot of Syrians,” he said. “This is supposed to be our enemy.”
While some Syrians still have reservations about receiving aid from Israel, he added: “It is not the monster they told us it was. People have started looking at it differently.”
Correction: July 20, 2017
An earlier version of this article mischaracterized Georgette Bennett, who founded the Multifaith Alliance. She is the daughter of Holocaust survivors, not a Holocaust survivor herself.