Mr Vieira was apparently killed in a revenge attack
Guinea-Bissau's army has said it will respect the country's democratic systems following the assassination of President Joao Bernardo Vieira.
Under the constitution, the speaker of parliament has now taken office, and must arrange elections within 60 days.
Mr Vieira, 69, is thought to have been killed by rebel soldiers in revenge for the death of the army chief of staff.
However, the army has denied there has been a coup and the capital Bissau is said to be quiet.
The African Union, the European Union and former colonial ruler Portugal have condemned the killings and called for a respect for the rule of law.
West African regional group Ecowas is due to hold an emergency summit about the crisis in Bissau on Tuesday.
Chairman Mohamed Ibn Chambas told the AFP new agency: "It's not only the assassination of a president or a chief of staff, it's the assassination of democracy."
Mr Chambas told the BBC that he would try to ensure that the constitution was respected.
The AU called the killings "cowardly and heinous attacks" and is reportedly arranging its own meeting over the situation, while Portugal has offered to assist in preserving order if needed.
Mr Vieira, nicknamed "Nino", was killed at his private house close to the presidential palace in Bissau.
His death came hours after chief of staff, Gen Tagme Na Waie, died in a blast that destroyed part of the military headquarters.
JOAO BERNARDO VIEIRA
Electrician by trade
Key figure in struggle against Portuguese colonial rule
1980: Came to power in coup, as head of armed forces
1994: Won country's first multi-party elections
1999: Overthrown after sacking army chief
2005: Returned from exile to win presidential election
After Gen Tagme's death, the army had ordered two private radio stations in the city to cease broadcasting.
Armed forces spokesman Samuel Fernandes told reporters at one station: "We are going to pursue the attackers and avenge ourselves."
Braima Camara, a reporter from privately-owned Radio Pindiquiti in Bissau, told the BBC the president had been shot and stabbed in retaliation after he admitted giving the orders for Gen Tagme to be killed.
The president's house was largely destroyed in the assault and later looted by soldiers, he said.
The cabinet has announced seven days of national mourning for both leaders and launched a judicial inquiry into the deaths.
In a statement on state radio following Mr Vieira's death, the military insisted no coup was in progress in Guinea-Bissau, one of the world's poorest states.
Naval Commander Jose Zamora Induta said the military "gave guarantees to the prime minister that it will remain faithful to democratic principles and respect for the constitution".
The national assembly speaker - Raimundo Pereira - has now taken over at the helm of a transitional government and must organise presidential elections within 60 days.
The president and army chief are said to have been at odds for months.
Guinea-Bissau has been plagued by coups and political unrest since it gained independence from Portugal in 1974.
President Vieira, just like the country's previous leaders, relied on the army to stay in power, and personal rifts made it a rocky relationship, the BBC's West Africa correspondent Will Ross says.
Guinea-Bissau is a major transit point for Latin American cocaine headed for Europe and some army officials are known to have become involved in the trade, our correspondent says.
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