An Islamist rebel sits at his guard post in the Syrian city of Idlib this week. (Ammar Abdullah/Reuters)

For months, U.S. military officials had been vetting the first unit of Syrian fighters slated to join a new force to be trained by the United States and allied nations. But when violence flared up in the unit’s home area, the fighters made a decision to stay home and defend their communities, forcing U.S military officials to line up an alternate unit.

That last-minute scramble delayed the launch of the training program by several weeks to sometime in May, military officials said. It is also a sign of the obstacles the United States and its allies face as they try to build a rebel force, from a distance, in the midst of Syria’s civil war.

A senior military official said that training preparations had been held up “due to the fluid environment in Syria” but were now moving ahead. Training sites will eventually be opened in Turkey, Saudi Arabia, Qatar and Jordan.

The official, speaking on the condition of anonymity to discuss military planning, said the alternate unit had been identified but not fully vetted when the first unit pulled out. “So it will take more time to prepare the support for this group,” he said.

On the eve of the program’s long-awaited launch, U.S. officials acknowledged it will have to overcome a host of challenges, including the relatively small size of the force that is being trained — up to about 5,000 fighters — and that they will return to a multi-sided conflict characterized by shifting allegiances and battle lines. A similar program, run covertly by the CIA, has not resulted in a visible impact on the war.

The program also presents Washington with a diplomatic test. Although U.S. officials say the purpose of the training, in keeping with a congressional authorization and White House policy, is to enable Syrians to defend themselves and to take on the Islamic State militant group, partner nations behind the training program are most interested in toppling Syrian leader Bashar al-Assad.

Through four years of bloody conflict, the United States has shied away from direct military confrontation against Assad, betting instead on now-stalled political talks. The White House only authorized military involvement in response to the rise of the Islamic State, which has grown strong amid Syria’s civil war.

“The president has made clear that ISIL is our priority,” said Ali Baskey, a White House spokesman, referring to the Islamic State. “The [Pentagon training] program is an important component of our broader counter-ISIL strategy.”

In February, Turkish Foreign Minister Mevlut Cavusoglu said the program would train fighters to face the Islamic State and the Assad regime, underscoring U.S. and Turkish differences over Washington’s reluctance to take on Assad. Officials in Saudi Arabia and Qatar, both important backers of the Sunni Muslim uprising against a regime supported by Shiite Iran, share that priority.

U.S. officials have sought to play down differences with their training partners and said that allied governments have acknowledged the U.S. focus on fighting the Islamic State. A State Department representative, who like other officials spoke on the condition of anonymity, said coalition partners were united in their “long-term goal” of a peaceful, post-Assad Syria.

“While there cannot be perfect alignment, we are certainly not at variance in our objectives going into this program,” a senior administration official said.

Such differences matter because they could lead to confusion if the new force ends up in direct conflict with forces loyal to Assad and allied nations differ over what help to provide.

Visualizing the 220,000 lives lost in Syria

“If the foreign backers of this new force themselves are not in agreement about the mission before it even deploys into Syria, that is a warning that the force itself could quickly run into problems,” said Robert Ford, a former U.S. ambassador to Syria under President Obama.

The administration has determined that existing legal authorities provide a basis to build and arm a force to fight the Islamic State, which has attacked Americans and their allies, but not to go on the offensive against the Syrian military.

None of the multiple armed groups fighting in Syria — including government forces, Lebanese Hezbollah fighters, Western-backed rebels and various Islamist factions — are close to a decisive victory. Although rebels led by the al-Qaeda-linked Jabhat al-Nusra seized the northern city of Idlib last week, Assad retains a strong power base in Damascus and other parts of the country.

“My feeling is that these guys will fight whoever they come up against,” a second defense official said, referring to the new U.S.-trained force.

Beyond conditioning future assistance, U.S. officials will have limited power to control how the new Syrian force uses its training and equipment.

U.S. officials are now debating whether they should commit to providing military protection for the fighters once they return to Syria.

Most senior officials at the Pentagon think they should. Last month, Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, suggested the training program would not succeed unless the fighters believed they had “a reasonable chance of survival.”

“Militarily, we’re prepared to provide intelligence, logistical and air support should this policy decision be made,” the military official said.

If approved, the Pentagon might provide the U.S.-trained force additional ammunition supplies, give them radios and phones, or share intelligence about the location of adversaries. When they’re pinned down, U.S. planes could provide air support.

It’s unclear which forces U.S. planes would be authorized to strike in defense of allied fighters in Syria. If they hit back against attacks from forces loyal to Assad, that could quickly draw the United States further into the war.

Fred Hof, a former senior State Department official now at the Atlantic Council, said the U.S.-backed force was sure to come into conflict with Syrian troops.

“I think even the U.S. is coming to the conclusion that an awful lot of the time spent on the ground in Syria will be fighting the Assad regime,” he said.