Staff at World Vision say the potentially-deadly procedure - which is considered a symbol of entering womanhood in some cultures - could take decades to completely wipe out from some areas of Kenya.
Marking the International Day of Zero Tolerance to FGM World Vision's national co-ordinator for gender and disability in Kenya, Phiona Koyiet, told Premier most pastors "do not understand that it is actually bad to do FGM."
She added: "They think it is a cultural practise that is right. So, even among the religious leaders, at times they do not have that information."
The prevalence of FGM among the Samburu (86 per cent), Masaai (78 per cent) and Pokot (75 per cent) communities in Kenya is far higher than the national rate of 21 per cent, according to the 2014 Kenya Demographic Health Survey.
Phiona Koyiet said: "It is so serious because we have lost children in the process of FGM. It causes bleeding to death and also it causes trauma among the children."
Approximately 450 churches have been working with World Vision to tackle gender-based violence through the Channels of Hope training programme.
Workshops educate pastors and Muslim imans about the dangers of FGM and promote the Alternative Rites of Passage programme where girls experience a safe 'graduation ceremony' to represent entering womanhood.
Phiona Koyiet explained: "After you've done the community dialogue, then the parents accept that they have now allowed their child to go through an alternative rite of [passage] which is normally a faith-based training, culminated by a ceremony where they bless those children."
Click here to listen to Premier's Alex Williams speaking with Phiona Koyiet: