Political upheaval in Mali this year was followed by separatist claims in northern Mali by rebel and al-Qaida movements.
The Economic Community of West African States has proposed a neutral force for Mali to restore security and territorial integrity. U.N. officials, however, have said force should be used as a last resort.
Rice, following a U.N. Security Council briefing, said terrorist and criminal activity, coupled with a growing humanitarian crisis, presented a "complex set of interrelated challenges" for the African area known as the Sahel.
"This threat demands better coordination of existing efforts across the Sahel to combat transnational crime and the proliferation of terror networks," she said. "We can only tackle these threats effectively, if, as many have said, we work together."
Cheick Modibo Diarra resigned as Mali's prime minister after he was arrested by pro-coup forces this week. Bakary Mariko, a spokesman for Mali's military, told the BBC that Diarra was getting in the way of transition efforts in the country.
"Eight months ago the prime minister was given the mission to help Mali recover its territorial integrity but unfortunately he has been working to stay in power indefinitely," he said.
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