A rebel fighter aims his weapon during clashes with Syrian pro-government forces in the Salaheddin neighbourhood of Syria's northern city of Aleppo on Dec. 11. (MEDO HALAB/AFP/Getty Images)

The U.S. government said Wednesday that it has suspended delivery of nonlethal aid to Syria’s rebels because an Islamist group has taken control of the warehouses where the supplies were stored, a seizure that exposed the rapidly shrinking authority of the moderate opposition factions backed by the United States and its Western allies.

The United States continues to supply humanitarian aid to Syrian civilians affected by the long-running conflict, and officials indicated that a covert program to provide small arms and ammunition to rebels in the southern part of the country was ongoing.

But the suspension of the supply of food, medical kits, trucks and communications equipment to rebels in the north illustrates the erosion of U.S. influence over the groups battling to topple Syrian President Bashar al-Assad. A growing number of rebel factions, disillusioned by the low level of Western support, have been aligning themselves with Islamist groups that receive more generous funding from Persian Gulf Arab states.

The recently created Islamic Front, which seized control of the warehouses, includes the biggest Islamist factions in Syria. The front’s expanding presence, and the fact that it is not affiliated with al-Qaeda, may leave the United States with little choice but to work with it, if Washington hopes to retain any influence over Syria’s opposition, analysts and rebel leaders say.

The cluster of warehouses, in the border town of Atmeh, was controlled by the opposition Free Syrian Army’s Supreme Military Council, which was tapped in June as the chief recipient of U.S. aid. More important than the relatively meager contents of the warehouses was the international legitimacy they conferred on the SMC and its leader, Gen. Salim Idriss, ahead of crucial peace talks due to begin in Geneva in January.

On Friday, the Islamic Front told fighters from the SMC that a group linked to al-Qaeda was preparing to attack the warehouses and that it could help defend the sites. Fighters from the Islamic Front then ejected the SMC rebels at gunpoint. It is unclear whether there really had been a threat of an attack, and some rebel factions have alleged that the Islamic Front’s warning was a ploy.

The warehouses contained food, including military ready-to-eat meals, medical kits, communications equipment and pickup trucks, typical of the items that the United States is supplying under a $16.9 million program, U.S. and rebel officials said. The buildings also contained sizable quantities of small-arms ammunition from an unknown source, according to an opposition figure close to the rebel fighters who spoke on the condition of anonymity because of the sensitivity of the subject.

“We’re obviously concerned” about the takeover of the warehouses, said Jen Psaki, a spokeswoman for the State Department. “We’re not prepared at this point to make a broad statement about what it means and what the long-term impact will be. We’re in close contact with the SMC. And we will see over the course of time what this means.”

The nonlethal assistance promised in the spring by the Obama administration has not made a significant difference in the rebels’ fighting capacity, which opposition leaders say may be one of the reasons that many fighters grew disillusioned with the SMC. Promised items such as body armor and night-vision goggles never materialized. Deliveries were disrupted by the takeover of territory along the northern border by the al-Qaeda-affiliated Islamic State of Iraq and Syria, which Washington has labeled a terrorist group.

The Islamic Front — which includes many Salafists — has been pressing for inclusion in the SMC, out of concern that it will not have any input at the talks in Geneva, according to rebel commanders involved in the discussions. The talks will be the first between Assad’s government and the opposition since the conflict erupted nearly three years ago.

Louay al-Mokdad, an SMC spokesman, criticized the U.S. aid suspension as premature, saying that he expected negotiations between the Islamic Front and the council to soon resolve the dispute over the warehouses.

“It was just a misunderstanding between brothers,” Mokdad said. “The American administration decision was a little bit rushed. We understand their concerns, but we hope they will rethink this decision.”

He said the council would welcome some form of merger with the Islamist factions. “We are open to everyone,” Mokdad said. “It’s time to be united against the Syrian regime.”

But the prospect of rebel unity is complicated by U.S. concerns about the relationships between some of the Islamic Front’s factions and terrorist affiliates such as ISIS and the somewhat-less-extreme Jabhat al-Nusra.

U.S. officials have held meetings with Islamic Front leaders in recent weeks to explore their views, rebel commanders and American officials say. The U.S. government now has to decide whether it wants to maintain some influence over Syria’s rebels, which means dealing with the non-al-Qaeda Islamists, or to surrender the battlefield to increasingly extreme Islamists over whom it has no control.

“If we keep these groups at arm’s length, what influence can we have?” said Andrew Tabler of the Washington Institute for Near East Policy. But, he added, “talking to them is one thing. Working with them is another.”

Anne Gearan and Greg Miller in Washington contributed to this report.