The coup's leaders announced on Friday that they had "deposed" the interim president, prime minister and army chief-of-staff, according to a statement.
An overnight curfew has been imposed by the self-titled "military command", with members of the toppled government ordered to surrender themselves to the army command.
The statement also confirmed that private radio stations had been shut down.
The military said that soldiers had arrested Carlos Gomes Junior, the country's prime minister and frontrunner to be the next president.
It said that he, along with interim President Raimundo Pereira and General Antonio Indjai, the army's former chief-of-staff, were safe and "under the control of the army".
The coup leaders said that they "did not have ambitions of power", and had toppled the government because of an alleged "secret deal" with neighbouring Angola involving 200 military trainers.
They alleged that the prime minister had signed a deal that would "annihilate Guinea-Bissau's armed forces".
International condemnation
The United Nations Security Council, meanwhile, has condemned the military action, urging "the immediate restoration of civilian authority", Susan Rice, the United States' ambassador to the UN said on Friday.
The United States also strongly condemned the military coup.
"We call for the release of all government leaders and urge all parties to reconcile their differences through the democratic process," Jay Carney, the White House spokesperson, said.
Jean Ping, the African Union's commission chief, condemned "outrageous acts which undermine the efforts to stabilise the situation in Guinea-Bissau and tarnish the image of the country and Africa".
The Economic Community of West African States (ECOWAS), a regional bloc, also condemned the coup.
Former colonial power Portugal criticised those responsible for the coup and rejected suggestions that there was anything untoward in the Angolan military presence.
Ban Ki-moon, the UN secretary-general, meanwhile, said that he was "extremely concerned" at the arrest of public officials.
He called on the armed forces "to immediately and unconditionally release all detainees and ensure the safety and security of the general population", spokesman Martin Nesirky said.
'National unity government'
Earlier, senior Guinea-Bissau army officers met with leaders of the country's political parties, telling them to consider forming a "government of national unity".
The army would maintain control over the defence and interior ministries in such a government, the AFP news agency reported.
"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.
General Antonio Indjai, the army chief-of-staff, was among those who attended, though it was later announced that he had been removed from his post.
Also present were General Mamadu Ture Kuruma, the army's deputy chief-of-staff, as well as the heads of the army, air force and navy, the army's spokesman and four colonels.No member of the African Party for the Independence of Guinea-Bissau and Cape Verde (PAIGC), the party whose government has been deposed, attended the meeting.
On Friday, heavily armed soldiers were patrolling the streets of Bissau. They were also gathered at the finance and justice ministries.
Gomes had been expected to win a April 29 run-off election for the presidency after his challenger Kumba Yala, a former president who was overthrown in a 2003 coup, said he would boycott the polls because of irregularities in the first round of balloting.
The special election had been arranged after Guinea-Bissau's president died in January from diabetes-related complications.
The five main opposition candidates, including Yala, had said during a joint news conference on Thursday evening that the boycott of the April 29 election would be in the name of justice.
The West African country has weathered successive coups, and attempted coups, since gaining independence from Portugal in 1974.
