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U.S. Special Operations troops are forming elite counterterrorism units in four countries in North and West Africa that American officials say are pivotal in the widening war against al-Qaida’s affiliates and associates on the continent, even as they acknowledge the difficulties of working with weak allies.

The secretive program, financed in part with millions of dollars in classified Pentagon spending and carried out by trainers, including members of the Army’s Green Berets and Delta Force, was begun last year to instruct and equip hundreds of hand-picked commandos in Libya, Niger, Mauritania and Mali.

The goal over the next few years is to build homegrown African counterterrorism teams capable of combating fighters like those in Boko Haram, the Islamist extremist group that abducted nearly 300 Nigerian schoolgirls last month. U.S. military specialists are helping Nigerian officers in their efforts to rescue the girls.

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“Training indigenous forces to go after threats in their own country is what we need to be doing,” said Michael Sheehan, who advocated the counterterrorism program last year when he was the senior Pentagon official in charge of Special Operations policy. Sheehan now holds the distinguished chair at the Combating Terrorism Center at the U.S. Military Academy.

As the U.S. military seeks to extend its counterterrorism reach in Africa, President Obama is expected to appear at West Point on Wednesday to emphasize a foreign policy that would avoid large land wars, like those in Afghanistan and Iraq, and instead stress the training of allied and partner nations to battle extremists on their own soil.

Since the attacks on Sept. 11, 2001, the United States has slowly built a multipronged counterterrorism strategy in Africa: It has carried out armed drone strikes in Somalia from its only permanent base on the continent, in Djibouti; backed African proxies and French commandos fighting Islamist extremists in Somalia and Mali; and increasingly trained African troops to combat insurgents.

Under the new Africa plan, the Pentagon is spending nearly $70 million on training, intelligence-gathering equipment and other support to build a counterterrorism battalion in Niger and a similar unit in nearby Mauritania that are in their “formative stages,” a senior Defense Department official said.

In Libya, the most ambitious initial training ended ignominiously last August after a group of armed militia fighters overpowered a small Libyan guard force at a training base outside Tripoli and stole hundreds of U.S.-supplied automatic weapons, night-vision goggles, vehicles and other equipment.

As a result, the training was halted and the American instructors were sent home.

“You have to make sure of who you’re training,” said Maj. Gen. Patrick Donahue II, the commander of U.S. Army soldiers operating in Africa. “It can’t be the standard, ‘Has this guy been a terrorist or some sort of criminal?’ but also, ‘What are his allegiances? Is he true to the country, or is he still bound to his militia?’ ”

The U.S. military uses conventional troops and elite Special Operations forces to train foreign armies all over the world. The tasks range from teaching basic marksmanship to more advanced counterterrorism tactics and techniques.

In the past decade, the Bush and Obama administrations put a premium on training and equipping foreign troops to combat terrorists and other Islamist extremists and persuaded Congress to approve funding for those programs.

The new program to train small counterterrorism forces in Africa resembles larger efforts by U.S. Special Operations troops carried out in Iraq and Afghanistan. Pentagon officials declined to comment publicly on the new program, but budget documents reveal some details.

For Mauritania, about $29 million has been set aside for logistics and surveillance equipment in support of the specialized unit.

For Niger, where the United States launches unarmed surveillance drones to fly over Mali in support of French and U.N. troops, the Pentagon is spending nearly $15 million on the country’s new counterterrorism unit. The funds are part of $39.5 million this year to train and equip the West African nation’s army as it struggles to stem a flow of insurgents across Niger’s lightly guarded borders with Mali, Nigeria and Libya.

J. Peter Pham, director of the Africa Center of the Atlantic Council, a policy research group in Washington, said the United States must make tough political judgments before investing in ambitious counterterrorism training programs. Pham cited the lessons of Mali, where U.S.-trained commanders of elite army units defected to Islamic insurgents that seized the north last year.

“The host country has to have the political will to fight terrorism, not just the desire to build up an elite force that could be used for regime protection,” Pham said. “And the military has to be viewed well or at least neutrally by a country’s population.”

U.S. counterterrorism officials also warn that without a commitment to support the specialized units, training can stall. “It’s very difficult, very challenging dealing with African forces,” said Rudy Atallah, the former director of African counterterrorism policy for the Pentagon. “You train them to a certain level, and then they can run short on gear, communications, even tires for their vehicles.”

American officials say trainees must be carefully screened and monitored for possible human-rights violations or shifting allegiances. “Any unit we train could be used to go after political opponents rather than al-Qaida,” said Frederic Wehrey, a senior policy analyst with the Carnegie Endowment for International Peace who has visited Libya frequently.

No episode is a more sobering reminder of these risks than the collapse of the U.S. counterterrorism training mission last August at Base 27, also called Camp Younis, a Libyan military installation about 15 miles from Tripoli, the capital.

The U.S. trainers issued the Libyans M4 automatic rifles, night-vision goggles, Glock pistols and armored vehicles. The Libyans took custody of the weapons and equipment and were responsible for safeguarding them in a warehouse at the camp, U.S. military officials said.

In a predawn raid on Aug. 4, gunmen believed to be from one of the local militias overpowered the Libyan guards and seized the weapons and equipment in the storage area, U.S. officials said.

The American trainers were not at the training camp when the raid occurred because they regularly stayed at a nearby villa that served as a safe house at night, U.S. officials said.

U.S. military officials briefed on the raid suspect that the theft was an inside job in which a Libyan officer or soldier tipped off some local Tripoli militia members about the matériel stored at the base. Much of the stolen equipment was later recovered, but not before news reports indicated that some of the pilfered weapons had shown up online for sale on the black market.

The episode abruptly ended a weekslong training course that American and Libyan officials had hoped would restart broader training efforts that were suspended after the attack on the American Mission in Benghazi on Sept. 11, 2012.

A former U.S. Special Operations officer said there was a broader lesson for any future Libya training mission: “The take-away here is they’re going to take a lot more adult supervision to make sure the checks and balances are in place, so you don’t have outside militia taking over.”

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