Militia fighters stole hundreds of American-supplied automatic weapons and other equipment in a raid on a Libyan base where the US was training local forces, bringing an abrupt end to the secretive program, a report said Tuesday.

Elite US troops have been tasked since last year with covertly forming local counterterrorism units in Libya, Mauritania, Niger and Mali, part of US efforts to widen the war against Al-Qaeda affiliates in Africa, The New York Times reported, citing American officials.

It has been financed in part with millions of dollars in classified Pentagon spending, the Times said, and involves instructing and equipping "handpicked" commandos in the four countries, with the hope the teams will eventually be able to take on fighters like Boko Haram.

But the initiative has endured several setbacks, notably in Libya, where the training was suddenly cut short in August last year when a group of armed militia fighters overpowered a small Libyan guard force at a training camp outside the capital Tripoli, the newspaper said.

As well as automatic weapons, the fighters seized night-vision goggles and vehicles, it added, saying that American instructors were promptly sent home. US officials are now looking for a more secure site to get the program going again.

"But last summer's debacle and the political upheaval in Libya since then have caused American officials to rethink how they select local personnel," the Times said.

The American trainers had issued the Libyans M4 automatic rifles and Glock pistols, and the Libyans were responsible for safeguarding them at a warehouse. But all were taken in the pre-dawn raid on August 4, believed carried out by a local militia that overpowered the Libyan guards.

The American trainers were not at the training camp at the time because they would usually stay at a nearby villa, leading to suspicions that the theft was an "inside job."

Much of the equipment was later recovered, but some news reports suggested at least some of the weapons had gone on sale on the black market, the report said.

"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," the Times quoted a former American Special Operations officer as saying.

The program in Mali has failed to get off the ground as the new civilian government struggles to recover from a coup.

The Pentagon, meanwhile, is spending nearly $15 million in Niger on a new counterterrorism unit there, the Times said, and $29 million in Mauritania.