A statement from the State Committee for National Security (GKNB) said Tekebayev had been charged with corruption and would be "held until 25 April" at a GKNB penitentiary facility.
The arrest of Omurbek Tekebayev following his arrival at the main airport early Sunday triggered a snap protest in the capital Bishkek that peaked at a thousand strong.
A smaller protest of around 500 people took place in the city on Monday, calling on President Almazbek Atambayev to release Tekebayev and even step down from office.
Atambayev is barred from running for another term at the upcoming presidential election in November.
Tekebayev, the leader of the parliamentary Ata-Meken party and a bitter adversary of Atambayev's, is being held in connection with an investigation into corruption at a key telecoms company.
Specifically, he is accused of accepting a $1 million bribe from a Russian businessman to ease the purchase of the company in 2010.
The Ata-Meken party has dismissed the criminal case "fabricated".
In Tekebayev's southern homeland of Jalal-Abad on Monday supporters attempted to block a main road, according to footage broadcast by private Kyrgyz media.
'Without any legal basis'
MP Kanybek Imanaliev told AFP that in the span of a week, separate criminal investigations have been opened "without any legal basis" against three party members.
Aida Salyanova, a former state prosecutor and one of the Ata-Meken MPs currently under investigation on graft charges said on Monday that the protests would go on "indefinitely" until Tekebayev is released.
Atambayev, who is scheduled to host Russian leader Vladimir Putin Tuesday, has so far refused to back down as tensions grow.
Speaking at a meeting with civic groups on Monday, he said there would be "no untouchables" and that the government would not be "strongarmed" into withdrawing charges against opposition members.
While ex-Soviet Kyrgyzstan is the most democratic country in a region dominated by long-ruling autocrats, it has also been the most politically volatile in recent times.
The Muslim-majority country experienced two revolutions that unseated presidents in 2005 and 2010 followed by ethnic violence that left over 400 people dead.
Both Tekebayev and Atambayev were members of the interim government that came to power after the second revolution in 2010.
But Ata-Meken strongly opposed a referendum on constitutional changes that passed in December with a strong push from Atambayev's office, while Tekebayev also called for the president to be impeached last year.
Atambayev is constitutionally restricted to a single six-year term and says he has no intention of easing into the office of prime minister, a position whose powers have been boosted by the recent constitutional changes.
Tekebayev has not announced his candidacy for the November 19 vote, in which two former prime ministers have already said they will compete.
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