Kaia called for authorities to "show some maturity and responsibility" and investigate the killings.
"If these people had been killed by thugs and criminals or even by al-Qaeda, you would have had an outcry," he said.
More than 450 bodies were found in the capital's City Mortuary, 11 in the eastern town of Machakos, and another 11 in the Rift Valley town of Naivasha, the KNCHR said in their report.
"Almost all the cadavers bear classic execution signs of a bullet behind the head exiting through the forehead," the report read.
Kaiai said they had several pathologist reports that proved the "execution-style" deaths of the men.
Police have dismissed the execution accusations as fodder for "horror movies".
"That is a very irresponsible statement. I do not know where they got the figures," Eric Kiraithe, Kenya's national police spokesman, said.
"This is a very weird piece of imagination that would have passed as horror movie. I would like Maina Kiai to produce a post-mortem report from an authentic doctor declaring the cause of death," he said.
Kiai told Al Jazeera that they received the dead body count from official police registers at the mortuaries.
The police declared months ago a war on the politically linked Mungiki religious gang.
The group was banned in 2002 after deadly slum warfare that claimed the lives of dozens of people.
Once a religious group of youths who embraced traditional rituals, authorities say the Mungiki sect has transformed into a ruthless gang blamed for criminal activities including extortion and murder.
Since March, the gang has been accused of murdering at least 43 people - beheading several of their victims - mainly in Nairobi slums and central Kenya.
However, Kaiai said there was no proof that the men killed were part of the Mungiki gang.
The claims come less than two months before the country holds a general election with Mwai Kibaki, the current president, seeking a second and final term in office.