Japhet Koome, the national police inspector general, told reporters that "people were hiring dead bodies and parading them to the media to taint the police's image."
He did not provide evidence or details to support the claim.
Rights groups say a number of people were killed during a series of protests in July that called for President William Ruto repeal a law that raised taxes and strained the already high cost of living.
The country's opposition coalition has said it plans to file cases against individual police officers at the International Criminal Court in a move that Koome described on Tuesday as "intimidation."
"Police will not be intimidated by threats to file cases against them at the International Criminal Court," Koome said, adding that police will "continue combating anti-government protesters with force."
Amnesty International Kenya and a medical and lawyers association both said at least 11 people were killed in the protests, most of them shot while running from police or trying to surrender.
A police watchdog, the Independent Medico-Legal Unit, said 35 people were killed by police across the country in demonstrations in July.
The opposition coalition said police killed 50 people during the protests and shared videos of people it said were victims of police brutality.
The claims of excessive police force come as Kenya considers leading a multinational force in Haiti to take on gang warfare in a plan that would send 1,000 Kenyan police officers to the violence-wracked Caribbean nation.
The United States, as this month's president of the United Nations Security Council, plans to put forward a resolution authorising the force. Some Haitians have expressed scepticism about the proposed plan.
