Obama taped the message Monday in Dakar, Senegal, as Air Force One was refueling on its way to South Africa for a memorial service honoring former President Nelson Mandela, who died last week.
Addressing his remarks to "the proud citizens of the Central African Republic," Obama said citizens have the power "to choose a different path" than violence.
Those who commit crimes should be arrested, Obama said, adding that the United States will support the efforts of African countries and the French to restore security and protect civilians.
The transport flights are expected to begin in a day or two, according to a senior defense official who was not authorized to speak by name about the planning and thus requested anonymity. The official said there would be no other U.S. troops on the ground except any air crew needed for the flights into the Central African Republic.
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AP White House Correspondent Julie Pace, aboard Air Force One, contributed to this report.