The whereabouts of President Malam Bacai Sanha are unknown but a TV channel says his office is quiet.
The situation is extremely unclear and telephone lines are not working. The country has had several previous coups.
Guinea-Bissau has also become a major centre for trafficking cocaine from Latin America to Europe.
National radio interrupted its programmes to play military music, which correspondent say is code for a coup.
Heavily armed troops attempted to gain access to the UN headquarters, where a former head of the navy had fled.
Former President Nino Viera was killed in March 2009 by a group of soldiers just hours after the army chief of staff was blown up by a bomb.
President Sanha won elections held three months later.
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