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The minister for democracy and development, Colonel Moussa Keita, said the government is withdrawing from the negotiations being held in Burkina Faso until Captain Moussa Dadis Camara has recovered enough to return to work in Guinea.
During an address on state television, Keita assured Guineans the military government is not giving up on regional dialogue aimed at resolving the country's political crisis.
One opposition leader accused the government of withdrawing from the talks to stay in power longer. Mamadou Bah Baadiko of the Union of Democratic Forces (UFD) called for the negotiations to move forward.
Opposition groups have called for Captain Camara and other military leaders to step down. Before the shooting, the junta said Captain Camara must be part of any transitional government.
Burkina Faso's president, Blaise Compaore, has been mediating the talks in Ouagadougou on behalf of the Economic Community of West African States (ECOWAS).
Captain Camara suffered head wounds when he was shot last Thursday in a dispute with one of his aides. Guinean officials say he is recovering and will soon address the nation.
The military ruler was shot in an argument with presidential guard chief Lieutenant Aboubacar Sidiki Diakite, known as "Toumba." The two men were apparently arguing over who should take responsibility for the killing of dozens of opposition protesters in Guinea's capital, Conakry, on September 28.
Toumba is still at large. The government has offered a reward for his capture.
Another top military leader, General Sekouba Konate, has taken charge of the country while Captain Camara recuperates.
Captain Camara seized power in Guinea last December, after the death of longtime President Lansana Conte.