Security forces in the central Asian republic stormed the home of Almazbek Atambayev, reportedly armed with rubber bullets rather than live rounds.
But Mr Atambayev's supporters took up arms to defend him, killing one officer and capturing six.
The former president said the captives would be released later on Thursday.
Mr Atambayev, who is still inside his compound on the outskirts of the capital Bishkek, is accused of corruption, which he denies. Parliament stripped him of immunity in June.
But he claims the charges against him are politically motivated, orchestrated by his former ally and successor Sooronbai Jeenbekov.
After the botched raid, state forces retreated from the residence to regroup, while more supporters of Mr Atambayev arrived and a standoff began.
Kyrgyzstan's parliament has been recalled to address the crisis.
President Jeenbekov has also ordered his government to undertake "urgent measures" - but has not specified what they are.
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He said Mr Atambayev had "grossly flouted" the law by "putting up severe armed resistance" to police.
What happened overnight?
The raid began late on Wednesday evening. Video footage appeared to show Mr Atambayev walking around in the open, shaking hands of supporters, when gunshots are suddenly heard and the crowd scatters.
According to Kyrgyzstan's national security committee (GKNB), special forces armed "only with rubber bullets" were undertaking a "special operation to detain" the former president on Wednesday.
As the troops moved in, the GKNB said, Mr Atambayev's supporters fired back with live ammunition.
But Mr Atambayev has taken responsibility for the shooting, saying only he had a gun.
The health ministry said 36 people were injured in the clashes in Koi Tash village, including several members of the security forces.
"A special forces officer was delivered [to hospital] in an extremely serious condition with a gunshot wound. Despite resuscitation attempts, he died," a health ministry statement said.
Local media reports say six other soldiers were being held by Mr Atambayev's followers shortly after the raid was repelled.
As night fell, roads leading to the compound were barricaded by Mr Atambayev's supporters while security forces regrouped nearby.
Witness Mirbek Aitikeyev, who posted footage of the raid on Facebook, told AFP news agency that some of those protecting Mr Atambayev had seized weapons from the special forces, who "retreated under the onslaught of the crowd".
"Atambayev is still at his home... there are rumours that additional forces will be sent. The people here are making preparations," he said.
A return to violence
By Abdujalil Abdurasulov, BBC News
The end of Almazbek Atambaev's presidency in 2017 was hailed as the first peaceful power transfer in independent Kyrgyzstan achieved through elections. But recent events show that violence was merely postponed for two years.
Sooronbay Jeyenbekov was seen as Mr Atambayev's hand-picked successor - but something went wrong, and Mr Atambayev fell out with the new president. Mr Atambayev retreated to his village house where he surrounded himself with his supporters. Yet many were still shocked when the operation to detain Mr Atambayev involving special forces started.
Military vehicles and ambulances speeding to the village, along with reports of a shootout, fuelled an atmosphere of fear. But the general public do not appear to support either side.
Many are angry that a conflict between two politicians is threatening stability of the entire country. "Don't be fooled that we're choosing between [Atambayev] and the current government. They're from the same flesh," wrote Azim Azimov, a popular blogger.
What's the context?
Kyrgyzstan is one of the Central Asian republics that became independent with the collapse of the Soviet Union in 1991. It is about two-thirds the size of the United Kingdom, but with a population of just six million - most of which are Turkic-speaking Muslims.
The country remains relatively poor, with a GDP per capita on par with Cameroon or Kenya. Dissatisfaction with the government has meant a lack of political stability since independence - the first two post-Soviet presidents were deposed after waves of mass protests.
Relations between Mr Atambayev and Mr Jeyenbekov soured after the transfer of power, and observers say Mr Jeenbekov moved to sideline his predecessor politically last year by removing Atambayev loyalists from positions of power.
Parliament stripped Mr Atambayev of his immunity 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 has ignored three subpoenas from the interior ministry.
But he is also accused of multiple incidents of corruption - all of which he denies. He has ignored orders to surrender to police for questioning, characterising them as illegal.