Bakhytzhan Kashkumbaev, 67, was arrested in May for "inflicting damages" on one of his parishioners through his sermons.
He spent about a month in a psychiatric clinic during his pretrial detention.
Late on October 7, a court in Astana ruled that Kashkumbaev could be transferred to house arrest due to his poor health.
But on October 8, police rearrested Kashkumbaev on new charges moments after his release from a detention center in Astana.
Kashkumbaev's lawyer, Nurlan Beisekeev, told RFE/RL that the second case against his client is related to alleged extremism.
Kashkumbaev, a Christian convert from Islam, and his supporters insist that the case against him is politically motivated.
Kazakh and international human rights organizations have urged Kazakh authorities to release him.