The decision by the Economic Community of West African States at a summit in Abidjan, Ivory Coast, comes after coups in both countries, the BBC reported.
Ivory Coast President Alassane Ouattara, the current ECOWAS chairman, said regional leaders were "confronted by the biggest ever threat to our democracy."
"A strong response and the commitment of our allies is more than ever vital so that the region doesn't fall prey to terrorism and international criminality," Ouattara said.
The BBC said 500-600 troops would be sent to Guinea-Bissau immediately.
No timetable was set for at least 3,000 regional soldiers who are to go to Mali where the transitional government is fighting rebels in control of the north.
ECOWAS told coup leaders in Guinea-Bissau they would face targeted sanctions if they didn't agree to the deployment of soldiers within 72 hours.
The army took power in Guinea-Bissau April 12 during presidential elections and interim President Raimundo Pereira and current Prime Minister Carlos Gomes Jr., who was expected to be elected president, were arrested.
Soldiers said the coup came in response to what they said were plans by Gomes to reduce the size of the army in the West African nation.
In Mali, a civilian government in the south is in place after last month's coup that overthrew President Amadou Toumani Toure shortly before he was due to be replaced in elections.
But in the north rebels -- the secular National Movement for the Liberation of Azawad and Ansar Dine, an Islamist group that has started to impose Sharia in some towns -- want to create a separate state.
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