Margulan Mukhambetov was flown to Almaty on October 10 and handed over to Kazakh border guards.
He was reportedly met by people in civilian cothes at the airport, but has not been seen or heard from since.
His relatives and rights activists believe he is being detained by security officials.
Mukhambetov is one of some 200 Kazakhs who are followers of the Muslim branch of Salafism who have sought asylum in the Czech Republic since 2006.
The Salafi group members in the Czech Republic say they would be persecuted in Kazakhstan, where Salafism is viewed by the government as
Czech authorities officially informed the Kazakhs in early October that they would be deported, saying that as Kazakhstan will chair the Organization for Security and Cooperation in Europe (OSCE) in January, it would not persecute its citizens for their religious views.
Meanwhile, the Czech Interior Ministry has refused to comment to RFE/RL about Mukhambetov's deportation.
It has decided, though, to extend the deadline for many of the Kazakhs who are seeking asylum until summer 2010.
Ministry officials attributed their decision to extend the deadline to the large amount of documents immigration officers have to process.
Meanwhile, the pro-presidential Atameken (Fatherland) party issued on November 1 a letter calling for an official investigation into Mukhambetov's disappearance.
The letter, from Atameken chairman Yerzhan Dosmukhamedov, also urges Kazakhs to boycott Czech-made goods and vacations to Czech resorts because of that government's treatment of the Kazakh asylum seekers.
Salafism is a Sunni Islamic movement that takes the first practitioners of Islam as exemplary models.
Salafis do not recognize other branches of Islam. It was banned in Tajikistan in January.