Bakiev also signed decrees ordering that the foreign, interior, and defense ministers, as well as the head of the National Security Committee, should keep their posts in Atambaev's administration.
Bakiev appointed Atambaev acting prime minister on March 29 in a bid to defuse a deepening standoff with opposition lawmakers.
Atambaev told parliament he will work with Bakiev to prevent Kyrgyzstan from sliding further into political crisis.
"I am not going to put up with corruption or any privileges, whomever they may be for," he said. "My task is to implement anticrisis management -- to reanimate the government as a body that governs the social and economic development of the country. I also realize that we have little time to do that."
Atambaev succeeds Azim Isabekov, who resigned on March 29, a day after Bakiev blocked his attempt to sack several ministers.
(with material from Reuters)