Three girls were rescued from undergoing circumcision in Kapyego, Marakwet East on Saturday morning.
Assistant deputy county commissioner Andrew Mutuma said police stopped the exercise after a tip off from residents.
"The circumciser and parents ran away and the girls were taken to the chief's office for protection," he said on Monday.
He said investigations have been launched as police pursue the suspects.
"Security agencies are on high alert to enforce anti-FGM law and stop any attempts to circumcise girls," Mutuma said.
At least 2,300 girls, according to civil society groups and chiefs, have undergone the cut in Marakwet East since November.
This is despite several anti-FGM sensitisation efforts by NGOs including the United Nations Population Fund, World Vision Kenya and Marakwet Girls Foundation.
Last week, Elgeyo Marakwet county commissioner Fredrick Ndambuki said hundreds of girls and women are hurting as the harmful practice continues.
Many women are reportedly forced to undergo the procedure, while some demand to be circumcised.
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"Girls should be protected and assured of education and bright future. We want to make sure that our girls are free to choose what they want to do in their life and ensure that they are of good health," he said.
He asked local administrators to be vigilant and arrest anyone subjecting girls and women to genital mutilation.