CIA activities in Somalia
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According to the Alliance for the Restoration of Peace and Counter-Terrorism. As the power balance shifted towards this alliance, the CIA program backfired and the militias of the Islamic Court Union (ICU) gained control of the country. Although the ICU was locally supported for having restored a relative level of peace to the volatile region after having defeated the CIA-funded Alliance for the Restoration of Peace and Counter-Terrorism in the Second Battle of Mogadishu, concerns about the growth and popular support for an Islamic country during the United States' War on Terror led to a new approach of the intervention of CIA, the United States military and Ethiopia's dominantly Christian government.
The use of the Ethiopian Army was seen by the United States as an awkward, but necessary way to prevent Somalia from being ruled by an Islamic government unsympathetic to American interests. In December 2006 State Department officials were issued internal guidelines such as “The press must not be allowed to make this about Ethiopia, or Ethiopia violating the territorial integrity of Somalia...”
In late 2006, the US State Department said Ethiopia was trying to stem the flow of outside arms shipments to the Islamists in Somalia. Ms. Hironimus added that Washington was concerned about reports that the Islamists were using child soldiers and abusing Ethiopian prisoners of war.
Covert action failed in 2006, in which an effort, run from the CIA station in Nairobi, Kenya, sent money to secular warlords inside Somalia with the aim, among other things, of capturing or killing a handful of suspected members of Al Qaeda believed to be hiding there. Some Africa experts is reducing overall stability by putting a premium on its effort to capture or kill a small number of high-level suspects. Increasing the funding for secular militias, allied as the Alliance for the Restoration of Peace and Counterterrorism may have triggered counterattacks by Islamic militias, who have been pushing back the secular troops. "This has blown up in our face, frankly," said John Prendergast of the International Crisis Group(ICG), who was a Clinton Administration official in the State Department and National Security Council.
Using local militias was seen as a way to avoid sending US troops. State Department officers, however, disapproved of the CIA effort, with one source saying "They were fully aware that they were doing so without any strategic framework," the official said. "And they realized that there might be negative implications to what they are doing." In 2006, Leslie Rowe, the deputy Chief of Mission in Kenya, signed off on a cable back to State Department headquarters that detailed grave concerns throughout the region about American efforts in Somalia. Around that time, State Department political officer, Michael Zorick, who had been based in Nairobi, was reassigned to Chad after he criticized, inside the government, Washington's policy of paying Somali warlords. The details of the American effort in Somalia are classified.
Somalia's interim president, Abdullahi Yusuf of the Transitional Federal Government (TFG), criticized American support for nongovernmental actors in May 2006, "We really oppose American aid that goes outside the government," he said, arguing that the best way to hunt members of Al Qaeda in Somalia was to strengthen the country's government. Prendergast agrees the approach had some success, According his organization, militiamen loyal to warlord Mohammed Deere, a powerful figure in Mogadishu, caught a suspected Qaeda operative, Suleiman Abdalla Salim Hemed, in April 2003 and turned him over to American officials. Prendergast said "I've talked to people inside the Defense Department and State Department who said that this was not a comprehensive policy," he said. "It was being conducted in a vacuum, and they were largely shut out."
The official US position is to urge a return to peace talks by warring Somali factions, but some officials have also said an Ethiopian invasion could be the only factor to prevent the Islamic Courts Union (ICU) complete takeover of Somalia. According to the ICG, Ethiopia only broke up only the most visible part of the ICU: the regional administrative authority in south central Somalia (including Mogadishu), which served essentially as a political platform for Hawiye clan interests. The militant Shabaab leadership, scattered throughout the country, threatening to wage a long war. A U.S. air strike on 8 January 2007 apparently wounded Aden Hashi ‘Ayro, a prominent Shabaab commander, and killed some of his guards but failed to destroy any top targets.
Jeremy Scahill in the August 2011 edition of the Nation magazine reported on the CIA's compound at Mogadishu's Aden Adde International Airport. According to Scahill, "the facility looks like a small gated community, with more than a dozen buildings behind large protective walls and secured by guard towers at each of its four corners...At the facility, the CIA runs a counterterrorism training program for Somali intelligence agents and operatives aimed at building an indigenous strike force capable of snatch operations and targeted “combat” operations against members of Al Shabab."  According to OSGEOINT, the construction of the CIA facility seems highly probable due to the other changes that have occurred around the airport since its reported construction. Open source satellite imagery show wall-secured areas added, including a wall surrounding the entire airport as well as hardened access control points (ACPs). Between 20 July 2010 and 22 August 2011, AAIA has had much of the vegetation cleared off from the perimeter, guard towers added every quarter mile on the Northeast boundary (--more frequent on the Northwest), a towed artillery element deployed, as well as additional structures erected throughout the secured sections of the airfield. In addition, it also appears that an unknown donor (probably the US) is in the process of adding a parallel taxi-way to the main aircraft apron further enhancing the capacity of the airfield.
In early January 2011, it was reported that the US, probably the CIA, hit its first target in Somalia with a drone strike. Recently, reporting from OSGEOINT suggests that this drone probably originated from Camp Lemmonier, Djibouti where engineers at the base constructed a dedicated drone support apron during the 2010-2011 period. The first strike in Somalia coincided with the confirmed deployment of a predator combat air patrol and a predator primary satellite link suggesting local command and control.
- John Goetz, Marcel Rosenbach, Holger Stark (2007-06-13), Taking the 'War on Terror' to Africa, Der Spiegel, Archived from the original on 2008-07-30, retrieved 2008-07-29
- Mark Mazzetti (December 27, 2006), "U.S. Signals Backing for Ethiopian Incursion Into Somalia", New York Times'
- Timberg, Craig (June 17, 2006), "Guns Finally Silent In Somalia's Capital: Islamic Militias Impose a Welcome Calm", Washington Post: A01
- Mark Mazzetti (December 27, 2006), "U.S. Signals Backing for Ethiopian Incursion Into Somalia", New York Times
- Mark Mazzetti (June 8, 2006), "Efforts by C.I.A. Fail in Somalia, Officials Charge", New York Times
- "Cia's secret sites in Somalia". The Nation. 12 July 2011.
- "Probable CIA Compound at AAIA Somalia". OSGEOINT. 15 January 2012.
- "Djibouti: RQ/MQ-1 PREDATOR Deployment Imagery Confirmation". OSGEOINT. 24 February 2012.