The base was seized on August 24 in the Haut Mbomou area of southeastern Central African Republic, Radio Ndeke Luka reported, quoting Ugandan Colonel Milton Katarinyebwa.
The officer denied reports that Ongwen was killed and said Ugandan forces will track him down.
Since 2005, Ongwen has been wanted by the ICC for three counts of crimes against humanity and four counts of war crimes.
Central-Africans, Ugandans and American soldiers have been tracking LRA leaders for several months, particularly Ongwen and Joseph Kony, the movement leader.
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