Police claim five people were killed by mobs on Friday for looting during "unauthorised" processions called to welcome Opposition leader Raila Odinga.
In a statement on Thursday, spokesperson George Kinoti said the five were stoned to death.
"We are however aware that sections of the mobs accompanying the NASA convoy, looted property and five persons were killed by stoning in different incidences," he said.
Reuters photographers had reportedly counted two bodies with gunshot wounds sustained in the violence as police tried to disperse Raila's supporters who walked alongside his convoy from the airport.
Interior ministry spokesperson Mwenda Njoka said he could not confirm the casualties.
"When the people are so unruly, you expect police to react to use reasonable force to get them out of the way," he told Reuters.
Police have denied claims that Raila's vehicle was shot at during the protests.
"No live ammunition was used by any officer," Kinoti added.
Additional information from Reuters