The arrest of self-styled religious leader Nurlan Motuyev late Friday follows a wave of opposition arrests in the Central Asian state.
A press officer for the GKNB security organ told AFP that Motuyev had been arrested for "calling Kyrgyzstanis to fight in Syria on the side of banned extremist organisations, and live according to Sharia law" during an opposition meeting on Thursday.
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Local media also reported Motuyev as saying that firebrand IS leader Abu Bakr al Baghdadi "would have torn the heads off" the Canadian operators of a controversial gold mine in the country of six million that has faced nationalisation calls.
Motuyev was speaking at a forum of the People's Parliament group that has called for President Almazbek Atambayev's immediate resignation and the creation of a new government.
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Atambayev on Saturday blasted the group as well as Western-funded NGOs for trying to "destabilise the country" in a speech to mark the Mothers' Day holiday held over from the Soviet era.
Three other members of the opposition group formed in April and viewed as a marginal political force were arrested on charges of plotting to overthrow the government earlier this week.
Motuyev was once nicknamed Kyrgyzstan's "coal king" after he famously seized a strategic coal deposit in the aftermath of the first of two revolutions in the country in 2005.
He founded the Union of Muslims of Kyrgyzstan after a brief stint in jail and ran for president in 2009.
Kyrgyzstan is typically recognized as Central Asia's most democratic country, although draft legislation targeting civic associations and sexual minorities has raised concerns of backsliding.
The economically troubled ally of Russia has seen two governments overthrown and ethnic violence claim hundreds of lives since it gained independence in 1991.
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