Prosecutors accuse 62-year-old Almazbek Atambayev of making illegal land purchases and of corruption, but he enjoyed immunity from criminal prosecution as a former head of state.
Kyrgyzstan's parliament, loyal to Atambayev's successor Sooronbai Jeenbekov, voted 103 to six in favour of lifting that protection.
Moves against Atambayev may lead to a major power struggle in Kyrgyzstan, which has seen a series of political crises and revolutions since gaining independence with the 1991 break-up of the Soviet Union.
Speaking to journalists on Wednesday, a defiant Atambayev said he would "stand to the end" against the charges.
"I am not afraid of anything in this world. I've been in jail, had attacks on my life, I was poisoned," Atambayev, who served as president from 2011 to 2017, said at his residence in the village of Koi-Tash near the capital Bishkek.
"If I submit to this mafia clan then maybe half the population of Kyrgyzstan will fall," he said in a reference to the Jeenbekov administration.
Several hundred supporters had gathered at Atambayev's residence in the foothils of Kyrgyzstan's Tien Shan mountains, where a nomadic yurt has been converted into a press centre and a venue for political gatherings.
Long in opposition, Atambayev became Russia-allied Kyrgyzstan's first elected president to hand over power peacefully in 2017, following revolutions in 2005 and 2010.
But he is also a symbol of the impoverished Central Asian nation's rough-and-tumble politics.
He was active in securing Jeenbekov's election victory in 2017 during a feisty campaign that saw a criminal case opened against the main opposition candidate, who Atambayev repeatedly smeared in public.
Atambayev said Wednesday that Jeenbekov had been a personal friend before the public fallout.
He said Jeenbekov should have been "an older brother to the government" as president, but instead had several Atambayev allies arrested, including 41-year-old prime minister Sapar Isakov, jailed on corruption claims.
Like Atambayev before him, Jeenbekov has been accused of using state organs to get rid of political opponents.
"Now I understand that this person only needed power," Atambayev said.
Jeenbekov, who hails from the south of the country, has accused his predecessor of seeking to dominate him.
Atambayev, a northerner, said he feared Jeenbekov's presidency has widened a longstanding regional rift that "wasn't a problem" during the last few years of his presidency.
Atambayev's critics, however, accuse him of exploiting north-south divisions to bolster his weakened public standing.
The conflict between the two men will be watched in Russia and China, whose political and economic interests in the country deepened during Atambayev's rule.
But Atambayev said he was not too concerned about the geopolitics.
"Of course I have the best feelings and relations towards the Russian leadership, but we need to focus on the situation inside the country," he said.
"Innocent people are simply being thrown in jail."