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.
Gen N'Canha instructed the population to "remain calm".
In addition to Embaló, the president's army staff and a number of ministers have reportedly been arrested.
Guinea-Bissau, with a population of just under two million people, is one of the poorest countries in the world. The former Portuguese colony has seen nine coups or attempted coups since 1980.
There have been two attempts to overthrow Embalo, the latest in December 2023.