Chadian soldiers march during Flintlock 2014, a U.S.-led international training mission for African militaries, in Diffa. Reuters

The United States is reportedly training commandos in four North and West African countries to help in the fight against al Qaeda affiliates and associates on the continent.

Launched last year, the secretive antiterrorism program is instructing and training handpicked commandos in Libya, Niger, Mauritania and Mali, The New York Times reported on Monday.

The program, which was financed in part with millions of dollars in classified Pentagon spending, is being carried out by trainers including members of the Army's Green Berets and Delta Force.

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

The program has already suffered setbacks, however, with the theft of military equipment, leading to the temporary suspension of the project in Libya.

During a commencement address Wednesday at West Point, U.S. President Barack Obama is expected to deliver a major foreign policy speech. The president is expected to advocate fewer land wars and more training of partners to tackle their own security threats.

Under a new Africa plan, the U.S. is spending nearly $70 million to build a counterterrorism network in Niger and nearby Mauritania, a senior U.S. Defense Department official told The Times.

The only permanent U.S. military base in Africa is in Djibouti, which has been used to launch drone strikes on Islamist insurgents in Somalia. The base has also supported the fight against militants in Mali and has assisted the Nigerian government in the search for nearly 300 schoolgirls abducted six week ago by Islamist extremist group Boko Haram.