"Despite resuscitation attempts, he died", it said in a statement.
A video posted online by an Atambayev supporter showed several cars being driven out of the former president's country house by security officials after what his party described as his surrender. One commando was killed and 52 people were injured during the operation.
Atambayev's supporters took six policemen as hostages, but released them on Thursday.
The issue of "ensuring security and order in relation to the situation which emerged on August 7, 2019" was on the agenda of the session, the press service of the presidential administration said. Just $5 a month.
Jeenbekov said during the security council meeting that Atambayev had "rudely flouted the Constitution and laws of the Kyrgyz Republic" by resisting detention.
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After Atambayev's immunity was rescinded, he repeatedly rebuffed requests from authorities to be questioned in connection with the corruption allegations and refused to obey a government subpoena.
Atambayev, in typical style, fired back in remarks of his own.
"His supporters stole weapons from the special forces, who retreated under the onslaught of the crowd".
As events unfold, confusion reigns but already there are a few threads that - in the aftermath - will need to be examined.
Atambaev has rejected all charges against him, saying they are politically motivated. "I am ready to answer any questions, because there was no corruption", he said.
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Almazbek Atambayev served as Kyrgyzstan's president from 2011 to 2017. But within months, Jeenbekov purged Atambayev loyalists from the cabinet.
Jeenbekov and Atambayev were once friends, and the former leader backed the incumbent in 2017 elections that marked an unprecedented peaceful transfer of power between heads of state.
Second: The failure of the first raid is deeply embarrassing for the state. "Eleven more people are being treated in special forces' medical facilities", a ministry representative said. They clearly did not anticipate the resistance encountered but also - given the nature of the injuries reported - were avoiding the use of deadly force, for example by using rubber bullets over live ammunition.
Meanwhile, Wednesday's raid left a police officer dead.
In July, he met in Moscow with Russian President Vladimir Putin. Russian interference in Central Asian politics is often assumed as a given. After the meeting, however, Putin spoke of the need for political stability in Kyrgyzstan and said "everyone should unite around the sitting president".
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