Gunfire erupted near a government building in Bissau where President Umaro Cissoko Embalo was thought to be attending a cabinet meeting.
The whereabouts of the president and prime minister are unclear.
West African regional leaders condemned what they called a coup attempt and urged troops to return to barracks.
One of the poorest countries in the world, the former Portuguese colony has seen nine coups or attempted coups since 1980.
Struggling with a massive foreign debt and an economy that relies heavily on foreign aid, the country has also become a transhipment point for Latin American drugs, leading it to be dubbed by some as Africa’s first narco-state.
While Mr Embalo won the December 2019 presidential election, he faced a last-minute stand-off with parliament before taking office the following February.
A reporter on the ground, Alberto Dabo, told BBC News that unidentified heavily armed gunmen had attacked the government palace while President Embalo was meeting Prime Minister Nuno Gomes Nabiam inside.
He said that two people had been killed and, according to “reliable sources”, the president and all the members of the government were still inside the palace “in the hands of” the attackers.
A security source who did not want to be identified told the BBC that gunmen in civilian clothes had opened fire and a police officer had been killed.
The military had regained control of the situation and it was now “calm”, he said, but he added that the whereabouts of the president and prime minister were unknown.
Condemning the violence, the West African regional group Ecowas said it held “the military responsible for the wellbeing of President Umaro Sissoco Embalo and members of his government”.
BBC
