Atambayev supporters held six officers hostage during the raids that left more than 100 people injured before the former president finally surrendered Thursday. He now faces corruption charges.
Prosecutors additionally charged Atambayev with hostage-taking and causing mass unrest, Reuters reported, citing state news agency Kabar.
National security chief Orozbek Opumbayev further accused Atambayev of planning to stage a coup, the news outlet report.
Atambayev, who was in office from 2011 to 2017, was stripped of the prosecution immunity he enjoyed as a former president in June. Authorities wanted to subpoena him as a witness in the unlawful release of a Chechen crime boss in 2013, the BBC reported.
The conflict highlights tensions between Atambayev and his handpicked successor, Acting President Sooronbai Jeenbekov. After Jeenbekov took office in 2017, he purged Atambayev loyalists holding powerful government positions, souring their relationship, according to the BBC.
Jeenbekov has also accused Atambayev of multiple counts of corruption, which Atambayev denies.
Kyrgyzstan is a republic in Central Asia that gained autonomy with the collapse of the Soviet Union in 1991. The nation’s first two presidents after independence were both driven from office by riots, and the latest violence has fueled concerns of more instability.
Russia, Kyrgyzstan's main sponsor and ally, has called for restraint.
While Russian President Vladimir Putin met with Atambayev last month, he has since publically endorsed Jeenbekov, Reuters reported.
The Associated Press contributed to this report.