Clinton met with AU Chairwoman Nkosazana Dlamini-Zuma in Washington.
Members of the AU announced support earlier this month for a regional force to restore security in north Mali. Militant groups, some of which are aligned with al-Qaida, claimed autonomy for northern Mali following a series of political upheavals early this year. Some of the Islamic rebels there are accused of war crimes.
Clinton said during her meeting that Washington "strongly" support the African Union's efforts in the region.
"We are working to support the AU's leadership with respect to the crises in Mali," she said.
Last week, the Economic Community of West African States announced that it submitted its plans for a regional deployment to Mali to the U.N. Security Council. As part of the program, ECOWAS said it was contributing $63 million to the Mali military for training and to "insulate it from politics thereby subordinating it to civilian control."
The French government, the former colonial power in Mali, said it would provide logistical and training support for the African mission.