The order followed Atambayev's request to be relieved of the post, said Nurlan Shakiyev, spokesman for President Kurmanbek Bakiyev.
However, a spokesman for Atambayev's Social Democratic Party, Edil Basailov, said Atambayev was fired "because he was interfering with efforts to manipulate the upcoming elections" for Parliament that are set for Dec. 16.
Bakiyev appointed Atambayev in February amid a political crisis in which opposition groups were calling for Bakiyev to resign over corruption and cronyism allegations.
In May, Atambayev lost consciousness for two days and later claimed he had been poisoned. He said he had received death threats connected with a government decision to nationalize a semiconductor plant.
Politics in Kyrgyzstan - where both Russia and the United States have military air bases - have been mired in squabbling for two years since Bakiyev came to power in the wake of the overthrow of longtime President Askar Akayev.