Joao Bernardo Vieira, 69, was assassinated in his home on Monday morning by soldiers. His death came just hours after the West African nation's top army official, General Batista Tagme Na Wai, was killed in a rocket and gunfire assault.
Media reports suggest Vieira's murder was a revenge attack.
"Just like the African Union, we are against the forceful change of power," Igor Lyakin-Frolov said.
According to military commanders, the military will respect the constitutional order and the parliamentary speaker will temporarily take charge of the country.
The Associated Press reported earlier that the president was assassinated by a "renegade group" of soldiers and the shooting was not part of a military coup.
African Union Commission chief Jean Ping also condemned the assassination and said that he "was deeply shocked at hearing about the murder of the president."
Vieira was the President of Guinea-Bissau from 1 October 2005 until his assassination on Monday. He had previously been in power from 1980 to 1999 before being ousted during a civil war. He made a comeback in 2005, winning that year's presidential election.
