Free Syrian Army fighters carry their fellow fighter after he was wounded on the front line in Aleppo's Sheikh Saeed neighbourhood Monday. (STRINGER/REUTERS)

The Pentagon on Wednesday denied reports that the latest batch of U.S.-trained rebels in ­Syria had defected and joined al-Qaeda, as officials sought to dispel suggestions of further setbacks for the troubled effort to build an effective local force against the Islamic State.

Earlier this week, shortly after a group of 71 U.S.-trained rebels returned to Syria after completing an American training course in Turkey, one of the commanders said to be with the group issued a statement dissociating the fighters from the Pentagon program and saying that it would operate as an “independent faction.”

The statement triggered rumors that the group had defected to the al-Qaeda-linked Jabhat al-Nusra, fueled by photographs posted on social media by Jabhat al-Nusra purportedly showing U.S. weapons that had been handed over by the Pentagon graduates.

The new reports came as U.S. officials search for ways to retool the Pentagon’s $500 million training program, which was supposed to prepare a reliable, moderate force to combat the Islamic State, but which has come to symbolize the shortcomings of the Obama administration’s handling of Syria’s protected civil conflict.

A fighter from the Free Syrian Army's Al Rahman legion carries a weapon as he walks towards his position on the front line against the forces of Syria's President Bashar al-Assad in Jobar, a suburb of Damascus, Syria, in July. (Bassam Khabieh/Reuters)

At the Pentagon, Capt. Jeff Davis, a military spokesman, said that U.S. officials were in touch with members of the U.S.-trained group, referred to as the New Syrian Force (NSF), and said reports that the fighters had joined Jabhat al-Nusra were false.

“We have no information at all to suggest that that’s true,” Davis told reporters. He said photos posted by Jabhat al-Nusra-affiliated Twitter accounts, which purported to show American weaponry provided by those fighters, had been “repurposed.”

U.S. Central Command, which oversees the training program, took the unusual step of issuing a statement to rebut the reports. “All coalition-issued weapons and equipment are under the positive control of NSF fighters,” the statement said.

The whereabouts and affiliation of the fighters was thrown into doubt following the statement by Anas Obaid, who was one of the leaders of the new group of Pentagon graduates. He said the group would continue to fight the Islamic State, but not in coordination with the United States. He also said the group had disowned its parent organization, Division 30, the larger rebel unit from which the Pentagon trainees have been drawn, and would call themselves Atareb Rebels, after the town where they are based.

Division 30 issued a statement saying that the unit had been unable to contact Obaid and warned he would be put on trial for “high treason” if the reports of his defection were true.

Charles Lister of the Doha-based Brookings Institution said it was possible the U.S.-trained fighters had been intimidated by Jabhat al-Nusra or other groups into denying their U.S. affiliation. “In that area of northern Aleppo, it’s Islamists who have dominance, so to come in as a U.S.-backed force, you are at a disadvantage to start with,” he said.

Later, Division 30, on its Twitter feed, denied that any of its weapons had been handed over: “The handover of weapons has not occurred — not a single piece of weaponry.”

Still, U.S. officials acknowledge that they have limited ability to track the movements of the U.S.-trained fighters, who are not under American command and control, and their arms.

The program, which has produced fewer than 200 fighters so far, has been plagued by setbacks. After the first round of training, some fighters were kidnapped by Jabhat al-Nusra; others were attacked, and the unit dissolved.

Last week, Gen. Lloyd Austin III, the Centcom commander, said fewer than five U.S.-backed fighters were then in Syria.

“If this second group has failed as dismally as the first, this could well be the nail in the coffin of the program,” Lister said.

Sly reported from Beirut. Thomas Gibbons-Neff contributed to this report.