The United States is breaking a 20-year arms embargo on Somalia by providing unauthorized intelligence training to regional governments and special-forces missions, according to a forthcoming United Nations report that discloses new details of the U.S. war against al Qaeda in the war-torn African nation.

The report, issued by the U.N.’s Somalia Eritrea Monitoring Group (SEMG) and reviewed by The Daily Beast, details three covert U.S. programs to aid local Somali security services in their fight against Al-Shabab, the Somalia affiliate of al Qaeda. It says Central Intelligence Agency officers are helping the government of Puntland, a semi-autonomous region not recognized by the U.N., and U.S. special forces are fighting alongside Puntland soldiers. It also says the U.S. hasn’t notified the U.N. of these activities, as is required by the terms of the embargo. The U.S. helped establish the embargo in 1992 when Somalia erupted in a civil war.

The report says 12 countries, including the U.S., aren’t complying with the arms embargo, having failed to inform the U.N. of cargo flights to supply various parties in the Somalia conflict. The country is one of the world’s most violent, lacking a functioning central government and overrun by warring militias, Islamist insurgents, and pirates who threaten large parts of the coast.

“We are trying to establish a norm of compliance with the sanctions regime on Somalia,” said Matthew Bryden, the head of the SEMG. “We can’t do that if members of the U.N. Security Council themselves are not compliant.”

Spokespeople for the Central Intelligence Agency, the National Security Council, the U.S. Mission to the United Nations, and the Pentagon all declined to comment on allegations made in the forthcoming SEMG report. Hillary Renner, a spokeswoman for the State Department’s Bureau of African Affairs, declined to comment on “military operations or intelligence matters,” but said that since 2007, the U.S. has given $106 million to support the Somali National Army. “This support is intended solely for the purpose of helping develop security-sector institutions consistent with the U.N.-supported political process in Somalia and in compliance with the arms embargo on Somalia. The Department of State has continued to submit notifications for its support to the SNA,” said Renner.

The report illustrates how President Barack Obama’s often-secret war against al Qaeda can sometimes conflict with his administration’s commitment to work cooperatively with the U.N. As recently as 2010, the administration said it wasn’t directly involved in Somali military operations. “The United States does not plan, does not direct, and does not coordinate the military operations of Somalia’s [Transitional Federal Government],” said U.S. Assistant Secretary of State Johnnie Carson in March 2010. “Further, we are not providing nor paying for military advisers.”

Yet press reports in recent years have alleged that the CIA has trained Somali intelligence officers and that U.S. military personnel and drones were helping the Somali Army in an offensive against Al-Shabab, the local arm of al Qaeda. An article in The Nation last year detailed CIA assistance to Somalia’s national-security agency and the existence of an intelligence headquarters and detention center known as the “pink house.”

Only recently did Obama publicly acknowledge direct assistance. In a June 15 letter to Congress, the president said, “[I]n a limited number of cases, the U.S. military has taken direct action in Somalia against members of al-Qa'ida, including those who are also members of al-Shabaab.” He didn’t provide specifics, saying only that the moves were intended to “counter the terrorist threat.”

The new SEMG report offers fresh details about U.S. training and aid to the Somali National Security Agency. The agency operates something called the “alpha group,” according to one U.N. official involved in the report, that is “used as proxy for U.S. intelligence operations” in areas controlled by the country’s Transitional Federal Government.

When the U.S. government was asked about an “alpha group” by the SEMG it responded in a May 7 letter that it “does not acknowledge any form of direct support to the Somali National Security Agency,” according to the report.

The SEMG usually compiles its report on the arms embargo every year. Past reports, including from 2007 and 2008, said the U.S. had notified the U.N. of its activities. “A number of foreign Governments are reportedly involved in training the National Security Agency,” the 2008 SEMG report said. “But only the Government of the United States has notified the Security Council that it is doing so.”

That appears to have changed. The 2012 SEMG report lists among the unauthorized U.S. activities direct support for the intelligence service and security forces of the government of Puntland, a semi-autonomous region of Somalia that is not recognized by the U.N.

Mohammed Abdirahman Farole, the media adviser to and son of Puntland’s president, said in an interview that the CIA provides non-lethal assistance to the Puntland Intelligence Agency. “They do not bring us weapons,” he said. “The CIA gives us intelligence training and equipment. This is part of the global fight against the terrorists.” Farole added that his father’s government would “welcome the United Nations to come to Puntland and collect all the weapons.” But, he said, until that happens, the Puntland forces would need to be armed to fight terrorists and pirates.

The report alleges the CIA has indeed been training its Puntland equivalent for ten years, including in Qaw, a small town on the outskirts of the Puntland port of Bosaso. The report alleges that Puntland trainees use the same shooting range as security contractors training a Puntland maritime police unit.

Also in the report are allegations that an unnamed U.S. intelligence agency is operating a fleet of four Russian-made Mi-17a helicopters to transport special forces from Camp Lemonier, a U.S. base in Djibouti, to locations in northeastern Somalia to fight alongside Puntland forces. This was first reported in the Somalia Report, a website that tracks intelligence and military developments in the country, which said the forces were deployed to fight pirates. The report says the U.N. has confirmation of this from a “reliable military source.”

The report also says there were 64 reports of activities of foreign jet fighters, helicopters, and drones in Somalia between June 2011 and April 2012. The report doesn’t say whether any of these were U.S. drones. The report says the African Union Mission in Somalia has complained about unidentified drones flying in Somali airspace. “Some of these reports concern attacks mistakenly targeting an [Internal Displaced Persons] camp and a humanitarian feeding center, targeted killings by drones of Al-Shabab commanders, and Special Forces covert operations in Somalia.”

Bryden, the report’s author, said his group began investigating these alleged U.S. programs in 2010 after discovering two private American operators of cargo planes, Prescott Support Co. and RAM Air Services, were registering flights into Somalia with the U.N. International Civil Aviation Organization.

“We didn’t know the full extent of it,” said Bryden. “All we had was confirmation that the flights took place.”

Spokesmen from Prescott Support Co. and RAM Air Services declined to respond to requests for comment.

“My answer to those running this program is if you want this to be a covert program, don’t notify the civil-aviation authorities of your flights,” Bryden said. “Our job is to investigate flights just like this. And the flights are what led us to ask questions and dig deeper about undeclared U.S. programs in Somalia.”