June 26, 2012  -- America's top commander in Africa revealed that the U.S. military has conducted spy operations all over the continent as part of the fight against international adversaries from al Qaeda-allied terror groups that target the homeland to suspected war criminals like Joseph Kony.

"Do we collect information across Africa? Yes, we do," U.S. Gen. Carter Ham, commander of U.S. Africa Command, said in a leadership conference at the Africa Center for Strategic Studies Monday.

In an attempt to clarify recent press reports that the U.S. military had set up "spy locations" throughout Africa, Ham said that U.S. troops do at times go on "short-term deployments of capabilities" in various African nations, but always with the permission of the host country.

Ham did not explain what exactly those capabilities are, but gave as an example the hunt for Joseph Kony, the notorious leader of the brutal Lord's Resistance Army -- a hunt the U.S. military has supported with the permission of four local governments. Last October, President Obama announced that 100 American special operations troops had been sent to central Africa to help track Kony.

"To have some intelligence collection capability that has the ability to monitor the areas in which we believe the Lord's Resistance Army is operating, to be able to see, to be able to listen, to be able to collect information which we then pass to the four nations, four African nations, which are participating, I think is a good way ahead," Ham said.

Ham's admission comes two weeks after The Washington Post reported that the U.S. military had secretly expanded its presence in Africa to include a network of small air bases used to spy on terrorist organizations there. According to the Post, the military uses small, unarmed turbo-prop planes disguised as private charters to carry out sensitive intelligence collection.

Part of that program appeared to have been revealed in February when the Department of Defense announced the deaths of four special operations servicemen near Djibouti. The four men died after their U-28 plane -- a "non-standard" surveillance aircraft similar in appearance to a private plane -- was involved in an accident.

Gen.: Future Role for US Military in Libya, 'Ideal' Position in Somalia

Ham echoed fears previously voiced by U.S. officials to ABC News about a possible foothold extremist groups like al Qaeda may be trying to make in Libya and elsewhere in Africa. AQIM, an al Qaeda offshoot based in northwestern Africa, has publicly said it has "benefitted" from the chaos in Libya already.

Ham said that the U.S. is working closely with officials in Libya to determine a future role for the U.S. military in the north African nation that will likely involve assistance but "certainly not a large military presence [and] probably no permanent military presence."

On the continent's eastern end, Ham said the U.S. has taken the "ideal role" in battling al-Shabaab, an al Qaeda-allied terrorist group based in Somalia. There, Ham said the U.S. is engaged in training, equipping and funding African military partners to beat back the terrorist organization, which counts among its members a number of U.S.-born jihadis.

"Not a large U.S. military presence, we think that would be counter-productive actually in Somalia, but rather applying the resources that we do have to help those countries that are willing to contribute to this effort," he said. "I think that's a pretty good model for us."

The Associated Press contributed to this report.

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