IG Joseph Boinnet has directed Rift Valley Regional Police Commander Edward Mwamburi to restore order in Kainuk.
Three people were killed on Sunday when bandits from one of the two warring communities attacked their rivals.
Clashes paralysed transport at the border for hours before police restored order.
“The Police Commander should use available resources to stop the violence and restore order to allow members of the public to lead normal lives,” Boinnet said via Twitter on Monday.
The IG further ordered the regional police boss start investigating people suspected to have caused the violence.
“We, therefore, call on members of the public to cooperate with police officers in an effort to deal with the rustlers who are out to wreck the peace and trust that the local residents have built amongst themselves,” he added.
On Sunday, West Pokot Governor John Lonyangapuo blamed police officers for failing to tackle the bandits.
“We are surprised by the behaviour of the officers from the other side who behave like people from another nation,” Lonyangapuo said.