The results were expected on Thursday – both Embaló and his closest rival Fernando Dias have claimed victory.
On Wednesday, witnesses in Bissau heard gunfire at around 13:00 GMT but it was not immediately clear who was involved in the shooting or if there were any casualties.
Hundreds of people on foot and in vehicles fled, seeking shelter as the shots rang out, the AFP news agency reported.
Later on, General Denis N’Canha, head of the military household at the presidential palace, read out a statement declaring a takeover.
He said officers had formed “the High Military Command for the Restoration of Order” and closed the border.