The abductions illustrate the challenges confronting the Obama administration as it seeks to marshal local insurgents to fight the Islamic State group, which it views as the biggest threat in the region.

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ANTAKYA, Turkey —

A Pentagon program to train moderate Syrian insurgents to fight the Islamic State group has been vexed with problems of recruitment, screening, dismissals and desertions that have left only a tiny band of fighters ready to do battle.

This tiny band, 54 in all, suffered perhaps the most destructive problem yet Thursday: Its leader, deputy and at least five others were abducted in Syria, just inside the border with Turkey where they had been training. The abductions were carried out not by the Islamic State group but by the Nusra Front, an affiliate of al-Qaida that is another Islamist extremist byproduct of the four-year Syrian civil war.

The abductions illustrate the challenges confronting the Obama administration as it seeks to marshal local insurgents to fight the Islamic State group, which it views as the biggest threat in the region.

Despite a prolonged effort, the Pentagon has had little success recruiting fighters who are not themselves radical Islamists. It is also having trouble signing up groups to take on the Islamic State group instead of the government of Syrian President Bashar Assad.

The moderates, at any rate, are bit players in a rebellion in which many of the most radical Islamist insurgents are better-funded, better-equipped and more motivated, participants said.

The setback for the U.S. effort in Syria comes just as the United States and Turkey have undertaken a joint plan to create an “Islamic State free-zone” in northern Syria, helped by warplanes flown from Turkish air bases. It presumably would be guarded and defended on the ground in part by successful trainees of the Pentagon’s program.

The biggest kidnapping prize Thursday was the leader of the trainees, a Syrian army defector who had been responsible for recruiting a pool of 1,200 rebels to the program.

In an interview two days before he was seized, the leader, Nadeem Hassan, spoke about the troubles he had faced.

After screening, just 125 recruits were invited to the first course. Of those, more than half were thrown out or quit.

The rest, he said, had yet to learn whether U.S. warplanes would defend them if Syrian forces attacked.

Hassan said the Americans, worried about the lack of recruits, were recalling men they had once rejected. Some, expelled on suspicion of embracing “Islamic State doctrine,” are unavailable: They have since died in Syria, he said, battling the Islamic State group.

Pentagon training courses in Turkey and Jordan have graduated only about 60 fighters, U.S. officials say, a reference to Hassan’s men.

The training is often at cross-purposes with a longer-running, covert CIA training program for fighters battling Assad. Toppling him was the original goal of the Syrian revolt, before the Islamic State group sprang from its most extreme Islamist wing.

Both programs have a common problem: Working with Americans makes recruits a target, not just of the Islamic State but also of the Nusra Front.

The Nusra Front dealt an even more serious blow to the CIA program last year, attacking and dismantling its main groups, the Syrian Revolutionaries Front and Harakat Hazm, and seizing some of their U.S.-supplied, sophisticated anti-tank missiles.

New details about the Pentagon training and its problems were revealed in interviews over several months with about two dozen fighters and commanders, and with several senior U.S. officials involved or briefed, who requested anonymity to discuss military planning.

Hassan said the Pentagon program had not provided night-vision goggles to counter the Islamic State group’s expert night attacks. Yet, he said Tuesday, trainers had been pushing his skimpy band to quickly join front-line insurgent groups, “so they can get results to show their bosses.”

Hassan’s trainees were mainly from villages within the 68-mile strip along the Turkish border that the moderate insurgents are supposed to seize, and had long been slated for deployment there. But, Hassan said, they are so few “they can barely cover 200 meters.”

Better-financed groups are luring recruits awaiting the next course; they make $225 a month, and with no budget, Hassan said: “I can’t buy them lunch.”

“The situation is bad,” he said.

Defense Secretary Ash Carter has acknowledged the shortfalls, citing strict screening standards, which have created a backlog of 7,000 recruits waiting to be vetted.

From the start, the Pentagon program was saddled with what most potential recruits see as a fatal flaw: It aims only at the Islamic State group, not Assad.

The border operation planned with Turkey has the same aim, U.S. officials insist. But they have not explained how it will have more success than the Pentagon in rallying fighters for a mission against the Islamic State group, also known as ISIS and ISIL.

“We can’t start like that,” said Abu Mahmoud, who commands a group called Liwa al-Haq. “Let’s finish off the oppression we are facing now. You can’t ask me to fight ISIS when the regime is pounding us with explosive barrels every single day.”

He spoke in April in Gaziantep, Turkey, near the Syrian border, just after having heard U.S. officials pitch the Pentagon program to 20 insurgent groups. Only four or five, he said, agreed to join. They were from Deir al-Zour and parts of eastern Aleppo province, places where the Islamic State group is the main threat. The government’s main presence there is aerial bombardment, while the front lines on the ground face the Islamic State.

Abu Mahmoud, who uses a nom de guerre for security, said he had considered sending 100 fighters but changed his mind on hearing that trainees would not fight government forces or get advanced weapons.

“What do I need training for?” he said. “Four years we’re fighting.”

Many Syrian insurgents — including conservative Islamists — agree. They are happy to fight the Islamic State group, but few are willing to forswear fighting Assad.

Several insurgent leaders said the Pentagon should market its program as “protecting civilians,” from both the Islamic State group and government forces. “It would be more convincing,” said Tayseer Darwish, an officer who defected.

Just two main clusters have joined the U.S. fight, according to many people involved, and they are marginal players acting on local considerations. One is from Deir al-Zour, an eastern desert province with little government presence where the Islamic State has massacred resistant tribes.

Nawwaf al-Basheer, their leader, said 1,100 men were ready, but training has been postponed until September.

Then there is Hassan’s group, mainly Turkmen, an ethnic minority, from a small patch of Aleppo province. For now, battlefield dynamics mean driving the Islamic State group from the area also hurts Assad. The Islamic State group has been attacking insurgents from the east, interrupting a rebel assault on the Assad-held half of Aleppo.

The Syrian military, which regularly bombards the zone, knows that, too, and could react. Turkish officials insist the area will “naturally” become a “safe zone” from government attacks. But U.S. officials deny such a commitment.

Hassan said he had asked his trainers “if they are going to protect us” and got a noncommittal reply.

Two days later, the kidnapping appeared to show just how vulnerable Hassan was.