The coup leaders announced Friday that the prime minister, interim president and army chief-of-staff general had all been deposed hours after the coup attempt was launched late Thursday.
They also imposed an overnight curfew, called on members of the toppled government to surrender to the army command and confirmed that private radio stations had been shut down.
The UN Security Council condemned the military action and urged “the immediate restoration of civilian authority”, US ambassador to the United Nations Susan Rice said after council talks on Friday.
The United States, Canada and Nigeria were among others joining the chorus of condemnation of the military coup.
“We call for the release of all government leaders and urge all parties to reconcile their differences through the democratic process,” White House spokesman Jay Carney said.
Washington also issued a travel warning for Guinea-Bissau, urging American citizens “to shelter in place and avoid the downtown area of Bissau.”
The African Union’s commission chief Jean Ping condemned the “outrageous acts which undermine the efforts to stabilise the situation in Guinea-Bissau and tarnish the image of the country and Africa.”
Guinea-Bissau army chiefs had earlier met leaders of the political parties, telling them to consider what they called “a government of national unity” in which the coup leaders would control the defence and interior ministries.
“The soldiers told us… to think about a government of national unity and its composition,” one party leader, who requested anonymity, told AFP after the closed-door meeting at the former military headquarters in the southern suburbs of Bissau, which lasted for more than a hour.
The chief-of-staff General Antonio Indjai was among those who attended, though it was later announced that he had been stripped of his post.
Also present were the deputy chief-of-staff, General Mamadu Ture Kuruma; the heads of the army, air force and navy; the army’s spokesman and four colonels.
The main political parties were represented at the meeting, except that there was nobody from what was, until Thursday night, the ruling African Party for the Independence of Guinea-Bissau and Cape Verde (PAIGC).
Deposed prime minister Carlos Gomes Junior, the favourite in a second-round presidential election set for this month, was seized in a military assault on his home using rocket-propelled grenades on Thursday evening.
The military also captured interim president Raimundo Pereira.
“The army confirms it has deposed the interim president Raimundo Pereira, the prime minister Carlos Gomes Junior and the army chief-of-staff General Antonio Indjai,” said Friday’s statement from the ruling “military command”.
“The three are safe and sound and are under the control of the army,” it added.
Indjai himself seized the post from his predecessor Jose Zamora Induta in an army mutiny in June 2010. At the time he was serving as his deputy.
Gomes had garnered 49 percent of the vote in the first round of the election on March 18 and campaigning for the second round was supposed to start Friday.
But on Thursday evening, soldiers armed with rocket-propelled grenades and Kalashnikov rifles launched their power grab. Gunfire and ambulance sirens echoed through a city plunged into darkness as electricity was cut off.
A military source said the arrested prime minister had been taken to army headquarters at San Vincente, 45 kilometres (28 miles) north of the capital, but the whereabouts of the president were not known.
Troops also seized the ruling party headquarters and the state radio station. On Friday, heavily armed soldiers were patrolling the streets of Bissau. They were also gathered at the finance and justice ministries.
West African regional group ECOWAS, still grappling with a putsch and rebellion in nearby Mali, also condemned the coup.
The coup leaders have already insisted they are not interested in power, stating that they acted because of an alleged “secret deal” with Angola, which has 200 troops in the country to help reform the military. They feared the Angolan force was secretly being built up.
Former colonial power Portugal, condemning the coup, rejected suggestions that there was anything untoward in the Angolan military presence.
In the days leading up to the coup, there had been fears of unrest in Guinea-Bissau, which has already suffered half a dozen coups or attempted coups since 1980.
The first round of the election had already been tainted by the assassination of former military intelligence chief Colonel Samba Diallo.
Diallo had been accused of involvement in a 2009 bombing that killed the then army chief and in turn prompted the murder of president Joao Bernardo Vieira in a revenge attack.
Since independence in 1974, Guinea-Bissau’s army and state have remained in constant, often deadly, conflict, and no president has ever completed a full term in office. Three have been overthrown and one was assassinated.
The country has also become a hub for drug-running between South America and Europe.