Shakirov said at an international conference in Astana on March 24 that the number of complaints about torture and abuse of power in prisons fell by some 50 percent in 2010 compared with 2009.
But he admitted that incidents of abuse of power with respect to prisoners did still occur.
Kazakh human rights defender Vadim Kuramshin told RFE/RL that he believed the situation is the opposite. He said that "people in prison are simply afraid to file appeals, as afterward their life becomes impossible."
Kuramshin added that the number of complaints he received from prisoners and their relatives within the last week "surpasses reasonable limits."
The acting director of the Kazakhstan Bureau for Human Rights, Roza Akylbekova, told RFE/RL that the decline in the number of complaints to the ombudsman "does not mean that the overall number of torture cases decreased."
She said her organization had information that proves the opposite of what Shakirov claims.
Ardak Zhanabilova, who chairs the Public Oversight Commission in Almaty, had earlier told RFE/RL about a trial of prison officers in Derzhavinsk who had been accused of torturing convicts.
She said the judge at the trial, which started on March 17 in Astana, did not allow human rights activists to attend the proceedings.
Many prisoners in Kazakhstan have been hospitalized in recent months after using knives and other objects to mutilate themselves to protest the overall poor prison conditions.