Unnamed diplomats told The New York Times that Vieira was shot by troops who blamed him for the death of army chief of staff Gen. Batista Tagme Na Wai, who died in an explosion Sunday night.
"Nobody knows who is in charge," one diplomat told the newspaper in Conakry, capital of the neighboring Guinea. "Nobody knows what the army will do."
Known as a transit point for South American cocaine shipments bound for Europe, the west African nation of Guinea-Bissau is a former Portuguese colony that has been wracked by instability in recent months.
Vieira, 69, was returned to power in a 2005 election after an earlier time as Guinea-Bissau's military ruler in the 1980s and 1990s, the Times said. His regime became increasingly unstable last year as reports of tensions between him and the military elite filtered out.
Vieira assembled a 400-member personal bodyguard that was accused in January of opening fire on the army commander, the newspaper reported.