General Verissimo Correia Seabra declared himself as the interim president on Sunday, as the country's deposed president and the prime minister were being held in the army headquarters.
"I am going to assume the presidency of the republic until there are elections," General Seabra announced.
His announcement came soon after the military seized power in a bloodless coup in the morning.
Commander Zamora Induta announced the coup over a private radio station, demanding payment of salary arrears and accusing Prime Minister Mario Pires of having failed the former Portuguese colony.
The new president, however, explained that he had no personal grudges against the deposed president Kumba Yalla.
"As a person, I have nothing against Kumba Yalla. He can stay in Guinea-Bissau as well as leave the country. Thats up to him," he said.
The army headquarters said the coup was staged because of the inability of the government to resolve the country's most pressing problems.
No gunfire was heard in the capital Bissau as the military took over. The coup came amid rising popular resentment over the postponement of elections five times since February.
The latest postponement came only on Saturday, when the electoral commission said it was unprepared to hold elections and needed time until November to complete voter registration.
Guinea-Bissau is a country of about 1.5 million people which gained independence from Portugal in 1974.
The military junta, which overthrew President Joao Bernardo Vieira in 1999, relinquished power to Yalla the following year after he won presidential elections.
Portugal, meanwhile, condemned the coup and called the military to allow elections to go ahead.
"The Portuguese government deplores the military coup d'etat that occurred today and calls on its perpetrators to immediately reestablish constitutional legality so that the democratic electoral process under way will not be further compromised," the Portuguese foreign minister said in a statement.