Armed forces chief of staff General Verissimo Correia, leader of last year's coup that ousted President Kumba Yala, and another unnamed officer were killed on Wednesday morning.
Heavily-armed soldiers took over key buildings before dawn and fired off rounds in the direction of the military headquarters in capital Bissau.
A diplomat said the protesters were mostly young recruits, among the 650 soldiers who were sent to Liberia in August last year as rebels closed in on the capital Monrovia.
Later in the day, talks began between the government, the United Nations and the leader of the renegade troops to broker a deal to pay the soldiers.
Guinea-Bissau is a poor country on
Africa's Atlantic coast
Prime Minister Carolos Gomes Junior said the morning unrest was mostly likely spurred on by opposition politicians.
Gomes heads the government that was elected in March, just six months after Yala's ouster from the presidency of the country wedged between Senegal and Guinea on Africa's Atlantic coast.
A diplomat said the UN mission in Liberia had released funds to Guinea-Bissau's central bank in August to pay the peacekeepers but the money has not yet been disbursed.
UN sources said peacekeepers are paid between $300 and $1300 per month.
Most of Guinea-Bissau's roughly 1.5 million residents live on less than one dollar a day.