The move was the latest by the Bush administration, which in the wake of the postwar chaos in Iraq, has increased its emphasis on trying to stabilize such countries.
A statement by White House spokesman Scott McClellan said the step would help countries prevent terrorists from operating inside their borders.
Putting Rice in charge appeared aimed at helping coordinate Pentagon activities with other agencies' and accelerating the U.S. response to crises.
"We want to be fast, we want to be effective," said Carlos Pascual, the State Department official who will run the program.
Bush, as a presidential candidate, took a skeptical view of U.S. engagement in reconstruction of other countries. As president, however, he has spearheaded efforts to help Afghanistan and Iraq, among others, recover from conflict.
Last March, the State Department set up a new office to manage the aftermath of war and try to prevent extremism from taking hold in desperate places.
On Tuesday, the Pentagon said it was elevating peacekeeping to a level comparable to war fighting and would increase training and take other steps so maintaining stability would be a core U.S. military mission.