In March, the National Liberation Front (PALIPEHUTU-FNL, Parti pour la libération du peuple hutu-Forces nationales de libération), which until then had been absent during the peace talks, said it was now willing to participate when independent brokers were present.
In April 2003, Domiti Ndayizaye was appointed President of the Provisional Government. He was the country’s 4th hutu president, and the deployment was a consequence of the Arusha agreement of 2001. His 3 hutu predecessors in the presidential post had ended their periods dramatically. 2 had been deposed by military coup, and one mysteriously died in a plane crash with Rwanda’s president in April 1994. According to Countryaah, a spokesman for the country’s main rebel group, the FDD, declared that the transfer of power was “irrelevant.” There is no difference between Buyoya and Domiti. They represent the same system, the same government ». He also urged the people not to be “distracted by the ceremony”.
In July, the most serious partisan attack in 10 years took place in Bujumbura. About 300 partisans and 15 soldiers were killed. Acc. Ignace Ntawembarira, governor of Bujumbura Rural – the province around the capital – had 40,000 forced to leave their homes during a week-long clash between Hutus and Tutsis. He further stated that most of the displaced persons were forced to sleep under the open sky, stressing that urgent international assistance was needed. Washington urged partisans to hold back on the attacks and instead begin peace talks with the government. Burundi’s army that had Bujumbura under control informed that many of the Hutu victims were children aged 11-15. The number of people killed during the conflict in the country has now passed 300,000.
However, on September 8, 2003, President Ndayizaye and the FDD signed the so-called Pretoria Protocol on Politics, Defense and Power Sharing in Burundi. Acc. the agreement, FDD was to have 40% of the posts in the officer corps and the general staff. At the same time, a new national police force was to be established, with FDD holding 35% of the seats. The FDD must have 4 ministerial posts, the vice presidential post in the National Assembly and 15 seats in parliament. An agreement was also reached on the distribution of governor posts, ambassadors and a large number of posts at the local level. As a result, FDD immediately entered into a ceasefire. However, the second rebel movement, the FNL continues to deny the process, and the legitimacy of the transitional government. In December, a donor conference was held in Pretoria to allow the African security force to remain in Burundi for the next two years.
In November, the government gave FNL a 3-month deadline to start peace talks. The FNL rejected the deal and the call for negotiations, declaring that it would negotiate well with the Tutsis, but not with a hutu like Ndayizeye. FNL spokesman Pasteur Habimana declared: “It is the Tutsis who are killing us”, referring to the Tutsi majority in the country’s army. He continued: “That’s why we should negotiate with them.” African leaders declared that the FNL should not be left outside the peace agreement.
That same month, partisans attacked Ndayizeye’s official residence in Bujumbura. Only material damage occurred. FNL claimed responsibility for the attack. Habimana declared that the attack was a retaliation for the military’s attack on several partisan positions, after the FNL had refused to participate in peace talks.
In December, the first meeting between FNL and Tutsi officers took place in a secret place in Kenya after the FNL refused to acknowledge Ndayizeye’s legitimacy. In the same month, Nkurunziza took over from the FDD as Minister of Good Governance in Bujumbura.
In May 2004, Nkurunziza withdrew from the ministerial post, however, emphasizing that this did not mean resuming the war. The FDD accused the government of not acting in a way that promoted a permanent peace. The party stated that in the 6 months following the ceasefire, it had not been involved in Ndayizeye’s administration. The incorporation of FDD’s partisans into the country’s army in November 2003 was not affected by Nkurunziza’s resignation.
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In June, 5,000 UN peacekeepers began their activities in Burundi in support of the peace process. About 2,700 UN soldiers from South Africa, Mozambique and Ethiopia remained in Burundi.