OUAGADOUGOU, Burkina Faso — The Burkina Faso military crushed the last remnants of a failed coup on Tuesday, storming the barracks of the elite unit that staged the coup 13 days earlier.
The military announced late in the evening that it had shelled and then seized Camp Naaba Koom II, the unit’s headquarters near the presidential palace here in the capital, Ouagadougou.
The action followed a tense standoff, with troops loyal to the country’s transitional government having surrounded the camp, the palace and other major buildings here.
Holdouts from the unit, the Presidential Security Regiment, had refused to surrender, even after the leader of the coup, Gen. Gilbert Diendéré, called for them to lay down their weapons.
Throughout the day, tanks and armored pickup trucks took up positions outside the palace and the barracks. Soldiers, armed with machine guns and rocket-propelled grenade launchers, were stationed around the national radio and television stations and at the airport, which was closed.
The government ordered residents to stay away from the neighborhood around the palace, known as Ouaga 2000.
On Tuesday night, General Diendéré told Agence France-Presse in a telephone interview that he feared “many deaths and injuries” in the operation, but there was no official confirmation of any casualties. General Diendéré said he had left the base, but he would not disclose his whereabouts.
The transitional government announced the end of the coup in a statement.
“The coup elements of the former R.S.P. remained unbending in their will to define the Burkinabe people,” the transitional government said, using the French initials of the Presidential Security Regiment. “Using delaying tactics in the expectation of foreign reinforcements and in the hope of an eventually rallying of internal support, these coup elements, surrounded by a group of die-hards, have held the daily lives of millions of Burkinabe people. Faced with a situation that had become intolerable for our people, and determined to turn this dark page in our common history, our patriotic Defense and Security Forces carried out their responsibilities successfully.”
The R.S.P. was created in 1995 by President Blaise Compaoré, who was toppled by a mass uprising last October after 27 years in power. Mr. Compaoré has been living in exile in Morocco
— he was scheduled to travel to Ivory Coast for medical treatment on Tuesday — but many of his associates and supporters remain active in political life.
The coup began on the night of Sept. 16 when officers of the regiment stormed the presidential palace and held the interim president, Michel Kafando, and the prime minister, Lt. Col. Isaac Zida, hostage, along with several cabinet members. The regiment announced that General Diendéré, a former chief of staff to Mr. Compaoré, had taken charge of the country.
But the revolt quickly began to fall apart. Protests erupted in the country’s major cities: Ouagadougou, Bobo-Dioulasso, Koudougou and Ouahigouya. Unions went on strike, shutting down the economy. The United Nations condemned the takeover, and the African Union suspended Burkina Faso’s membership.
Mr. Kafando — along with Colonel Zida, who helped lead the uprising last October — was formally reinstated last Wednesday after a mediation effort by the presidents of Senegal and Benin, along with other leaders of the Economic Community of West African States.
Under the agreement brokered by the leaders, the R.S.P. was supposed to return to its barracks and disarm. General Diendéré publicly apologized for the coup and urged his followers to comply, but many in the 1,300-member regiment refused.
On Monday, the government declared the situation to be at an impasse and accused the regiment of soliciting help from “jihadists.”
Western governments worry that Islamist extremist groups, including Al Qaeda in the Islamic Maghreb, may infiltrate Burkina Faso from its northern neighbors, Mali and Niger.
In a radio interview on Tuesday, General Diendéré said, “I categorically deny this accusation.” He said that he accepted the decision to disband the R.S.P. and that he had tried to defuse the standoff, which he attributed to “rogue elements.” He noted that prominent officers in the regiment — including Commandant Abdoul Aziz Korogo, the unit’s interim commanding officer, and Capt. Abdoulaye Dao, its spokesman — had agreed to withdraw from the camp, along with scores of other members.