Atambayev's dramatic detention after two raids on his compound on Thursday saw one officer dead and six officers held hostage by his supporters before he finally surrendered.
Some 80 people were injured and 53 others hospitalized during the operation.
The general prosecutor said on Tuesday that Atambayev had been charged with "unlawfully carrying a weapon", "murdering a special forces officer", "taking hostages" and "organising mass unrest", the BBC reported.
The head of the National Security Services, Orozbek Opumbayev, said the former leader had the "intention to organise a state coup".
The Central Asian state has seen two revolutions in less than two decades and is caught in an escalating conflict between the former President and his successor Sooronbai Jeenbekov.
Atambayev served as President of the former Soviet republic between 2011 and 2017. Current President Jeenbekov had initially been a protege of Atambayev but the two have since fallen out.
Relations between the two soured after the transfer of power and observers say Jeyenbekov moved to sideline his predecessor politically in 2018 by removing Atambayev loyalists from positions of power.
Parliament stripped Atambayev of his immunity in June so that he could be sent a subpoena to appear as a witness in a case involving the unlawful release of a Chechen crime boss in 2013. He ignored three subpoenas from the Interior Ministry, the BBC said.
But he is also accused of multiple incidents of corruption - all of which he denies. He has ignored orders to surrender to the police for questioning, calling them "illegal".
Kyrgyzstan is a Central Asian republic that became independent with the collapse of the Soviet Union in 1991.
( With inputs from IANS )