Heavy gunfire was heard Thursday at the Bissau residence of outgoing Prime Minister Carlos Gomes Jr., who failed to win last month's presidential election outright, the BBC reported Friday.
Gomes' whereabouts were unknown, as was the location of interim President Raimundo Pereira, the BBC said.
The Economic Community of West African States condemned what it described as a coup attempt.
"What I can say at this moment is that ... the situation won't be accepted by ECOWAS," Ivory Coast Foreign Minister Daniel Kablan Duncan said.
Witnesses told the BBC state broadcasters remained silent Friday but people had begun venturing outside and soldiers no longer were present.
An emergency election was called in March to replace President Malam Bacai Sanha, who died in January following a long illness. Former President Kumba Yala, who placed second in the balloting, said he would boycott a runoff scheduled for April 29. He said last month's election was riddled with fraud.