“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.