Police spokesman Eric Kiraithe dismissed the allegation of police executions of suspects as "outrageous".
The Kenya National Human Rights Commission (KNHRC) had made the claim after investigating incidences of dead bodies being dumped around the capital.
In June, the president ordered police to hunt down Mungiki sect members blamed for a series of grisly murders.
"Even if you hide, we will find you and kill you," President Mwai Kibaki had said in a warning to members of the quasi-religious sect which was outlawed in 2002. vMungiki followers have been demanding protection fees from public transport operators, slum dwellers and other businessmen in and around Nairobi.
Those who refuse are often brutally murdered.
Arrests
Mr Kiraithe said KNHRC's allegations were a plot to discredit the government in the run-up to the December elections.
We have found signs of cars being driven to secret locations... gun shots, then dead bodies and food for the hyenas KNHRC's Hassan Omar
Reuters news agency reports that more than a dozen bloodied bodies have been dumped in bush on the outskirts of Nairobi in the past week.
The state-sponsored KNHRC has been investigating whether these and other killings were the victims of police executions.
KNHRC commissioner Hassan Omar said the organisation had reports of "cars being driven to secret locations with suspects" followed by "gunshots, then dead bodies and food for the hyenas".
Mr Omar said some of the latest victims may have been innocent of any crime.
But Mr Kiraithe insisted that police officers followed the rule of law when dealing with suspects.
After the president's directive, police raided the Nairobi slum of Mathare to arrest hundreds of suspected sect members.
At least 30 people died in gun battles with police during that operation, leading the human rights organisation Amnesty International to call for an enquiry.
