The KNCHR has accused the government of extra-judicial killings, torture and illegal detention.
In a report dubbed "The Era of Fighting Terror with Terror", security agencies are accused of 25 executions and 81 forced disappearances when carrying out crackdowns against terror suspects.
"Over 125 cases of illegal detention, torture and arbitrary arrest were also reported," vice chairman George Morara said on Tuesday.
Arrests are carried out with impunity and in “contravention of the law”, with suspects subjected to electric shocks, sleep deprivation and exposure to extreme heat or cold among others.
Agencies involved include the Kenya Defence Forces, National Intelligence Service, Border patrol, Kenya Wildlife Service and the Anti-Terror Police Unit.
The Kenya National Commission on Human Rights report also says torture chambers exist in military camps at Mandera, Garissa and Lamu.
Morara said the commission faces challenges of intimidation of witnesses, as well as being denied access to information.
"This is tied to the denial of access to the places of detention particularly those controlled by KDF," he said, adding that torture of innocent persons has risen in the last two years.
"Human violations were recorded in Nairobi, Mombasa, Lamu, Tana River, Wajir, Mandera and Garissa."
The report recommends the Independent Police Oversight Authority to investigate reported cases and forward the findings to the Director of Public Prosecutions.
KNCHR asked the government to assure Boni forest residents of their protection from security personnel.
On Monday, a leaked report from KNCHR said police conduct brutal and dehumanising operations against suspected terrorists.
The findings revealed suspects where their bodies might never be seen.