Esergepov's wife, Raushan Esergepova, told RFE/RL she thinks the commission, in the southern Kazakh city of Taraz, made the decision under pressure "from above."
Esergepova said the prison commission ruled on January 12 to parole Esergepov, who has served one year of his three-year sentence. But she added that the same commission held a second meeting on January 23 and ruled to keep Esergepov in jail.
Taraz prison officials refused to comment on the decisions and told RFE/RL to send a formal inquiry.
Esergepova said she received a letter from Deputy Prosecutor-General Askar Sekishev in December that said Esergepov has the right to be paroled after having served one-third of his prison term.
Esergepova said she will appeal the commission's negative decision to the Prosecutor-General's Office.
Rozlana Taukina, the head of the Kazakh nongovernmental organization Journalists in Trouble, told RFE/RL that it will protest against the commission decision, which she called "another subjective and prejudiced decision against a journalist who criticized the security services."
Esergepov was found guilty of revealing state secrets and sentenced to three years in prison one year ago. His supporters and rights organizations say the case against him is politically motivated because of his independent newspaper, which has stopped publishing since his arrest.