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The U.S. Africa Command (AFRICOM), an organizational construct intended to unify the entire African continent (except Egypt) under a single U.S. commander, is due to become fully operational September 30. As described by the Pentagon, it will be a new sort of animal, a combatant command “plus,” that will have the ability to mount military operations, but which will rely primarily on “soft power.” AFRICOM “will support, not shape, U.S. foreign policy on the continent,” Theresa Whelan, the Pentagon’s deputy assistant secretary of defense for African affairs, told a House subcommittee on Wednesday. But despite official assurances, concern is mounting that AFRICOM could stray from its “supporting” role to become the new center of power for U.S. activities in Africa. The issue is central to the ongoing debate over the new command’s proper place.

At this week’s hearing of the House Subcommittee on National Security and Foreign Affairs, the first of two scheduled hearings on AFRICOM, General Michael Snodgrass and Ambassador Mary Yates, both members of the command’s nascent leadership, assured lawmakers that AFRICOM is “a listening, growing, and developing organization dedicated to partnering with African governments, African security organizations, and the international community to achieve U.S. security goals by helping the people of Africa achieve the goals they have set for themselves.” And to its credit, AFRICOM has gone out of its way to calm fears that it represents a new imperial push into the Dark Continent. (It even hosts a blog to keep the public informed of its progress.) AFRICOM’s primary purpose, say proponents, will be to coordinate with the State Department and USAID in the pursuit of “stability operations”—one of the Pentagon’s latest enthusiasms, encoded in Directive 3000.05, which places humanitarian and relief operations on a level plane with combat missions. (You can read my earlier piece on the subject here.)

But even AFRICOM’s good intentions cannot disguise the geopolitical realities that compelled its creation. It’s not about doing good works in impoverished countries for their own sake; It’s about national interest. Countering China’s growing military and economic influence in Africa and assuring access to some of the world’s last remaining oil reserves top the list. (The United States now imports just as much oil from Africa as it does from the Middle East.) Terrorism also figures into the equation—primarily the elimination of ungoverned spaces terrorists might call home.

Not that these are unreasonable goals. On one level, the U.S. military’s ability to adapt is impressive. But problems could arise if AFRICOM begins to lead policy rather than follow it. A report released yesterday by Refugees International shows that, in the years since 9/11, the Pentagon’s slice of the nation’s foreign aid budget has ballooned at the expense of more traditional providers, like USAID. From the report:

Although several high-level task forces and commissions have emphasized the urgne need to modernize our aid infrastructure and increase sustainable development activities, such assistance is increasingly being overseen by military institutions whose policies are driven by the Global War on Terror, not by the war against poverty. Between 1998 and 2005, the percentage of Official Development Assistance the Pentagon has controlled exploded from 3.5% to nearly 22%, while the percentage controlled by the U.S. Agency for International Development (USAID) shrunk from 65% to 40%.

As for foreign military financing, the Pentagon’s bread and butter, “more than half of the FY09 budget request… is for just two countries—Djibouti and Ethiopia—considered key partners in the continental War on Terror.”

AFRICOM has countered criticism of its “militarization” of foreign aid with reminders that its command structure will include representatives of other federal agencies, such as State and USAID, to ensure that policy is still guided by civilian authorities. This, for example, explains Ambassador Yates’ appointment as “deputy to the commander for civil-military activities.” But though the Pentagon had planned for 25 percent of AFRICOM’s headquarters staff to come from federal civilian agencies, it recently revised the requirement down to just 4 percent, citing difficulty on the part of partner agencies to spare staff for inter-agency assignments. As the GAO’s John Pendleton told the House subcommittee:

Although DOD has often stated that AFRICOM is intended to support, not lead, U.S. diplomatic and development efforts in Africa, State Department officials expressed concern that AFRICOM would become the lead for all U.S. government activities in Africa, even though the U.S. embassy leads decision-making on U.S. government non-combat activities in that country. Other State and USAID officials noted that the creation of AFRICOM could blur traditional boundaries among diplomacy, development, and defense, thereby militarizing U.S. foreign policy… Nongovernmental organizations are concerned that this would put their aid workers at greater risk if their activities are confused or associated with U.S. military activities.

Such concerns are overblown, says Whelan. “The intent is not for DOD generally, or for [AFRICOM] at the operational-level, to assume the lead in areas where State and/or USAID have clear lines of authority.” Instead, AFRICOM will simply “allow the DOD to better coordinate its own efforts, in support of State Department leadership, to better build security capacity in Africa.”