It was the ninth coup in west and central Africa in five years and continued a pattern of instability in Guinea-Bissau, a notorious cocaine transport hub with a long history of military interventions in politics.
The self-styled "High Military Command for the Restoration of Order" announced in a televised statement on Wednesday that they had ousted President Umaro Sissoco Embalo.
They said the move came in response to a destabilisation plan involving politicians and drug barons, without going into more detail.
The army said Nta would serve for one year, Radio France Internationale reported.
Video on state media showed Nta, wearing a military uniform, raising his right hand to be sworn in during a ceremony attended by other military officials.
The takeover came a day before provisional results were due to be announced in the race between Embalo and Fernando Dias, a 47-year-old political newcomer who had emerged as Embalo's top challenger in the presidential race.
Ahead of the coup announcement, witnesses said gunfire rang out in the capital Bissau for about an hour near the electoral commission headquarters and presidential palace.
Embalo called French media to say he had been deposed.
The officers did not say if they had taken Embalo into custody, and there were no announcements about his whereabouts on Thursday.
African Union chairman Mahmoud Ali Youssouf condemned the coup in a statement on social media, and called for the immediate and unconditional release of Embalo "and all detained officials".
Heads of state from the regional bloc ECOWAS also condemned the coup and voiced concern over the reported arrests of Embalo, senior officials and electoral personnel.
Central Bissau was mostly quiet on Thursday, with soldiers on the streets of the capital and many residents staying indoors even after the overnight curfew lifted.
Businesses and banks were closed.
Dias had accused Embalo in a video statement of staging a "false coup attempt" to derail the election because he feared he would lose.
In a statement to Reuters on Thursday, the coalition backing Dias demanded that authorities be allowed to release results from Sunday's presidential election.
The coalition also called for the release of former prime minister Domingos Simoes Pereira, defeated by Embalo in the 2019 election.
He was detained on Wednesday, according to relatives and security sources.
Security forces used tear gas to break up a small protest outside the building where Pereira is said to have been detained, a Reuters witness said.
They also broke up a gathering near Dias's home on the outskirts of Bissau and two witnesses told Reuters that live rounds were fired.
There were no reports of casualties related to the violence on Wednesday or Thursday.
Guinea-Bissau is a small coastal country situated between Senegal and Guinea that is a notorious transit point for cocaine bound for Europe.
Under Embalo's administration the cocaine trade appeared to boom.
The country has been shaken by at least nine coups and attempted coups between 1974, when it gained independence from Portugal, and 2020, when Embalo took office.
Dias had campaigned partly on the promise of getting the military to stop intervening in politics.
Embalo has said he has survived three coup attempts during his time in office.
His critics have accused him of manufacturing crises as an excuse for crackdowns.
Election observers from the African Union and ECOWAS expressed "deep concern" over the coup announcement, adding that officials in charge of the electoral process had been arrested and called for their immediate release.
Nigerian former president Goodluck Jonathan, who had been observing the vote as part of the West African Elders Forum, was not reachable on Thursday, ECOWAS spokesman Joel Ahofodji told Reuters.
"I wouldn't say that he (Goodluck Jonathan) and others are trapped in Guinea-Bissau but we don't know his whereabouts," Ahofodji said.
Edwin Snowe, a senator from Liberia who had been among a group of parliamentary observers, told Reuters he left the country on Tuesday and had been unable since Wednesday to reach fellow observers who were still there.
