Both groups have been arguing over who owns more than 150 acres at Kitere in Rongo and Rapogi in Uriri subcounty.
The dispute began after the government launched a new initiative to reclaim land that used to belong to defunct local authorities.
The county administration says the Rapogi and Kitere plots were given to the Church by the council many years ago.
But the Church says it has all the necessary documents to prove its ownership, according to local paper, The Star.
The team was formed over the weekend after Governor Okoth Obado held talks with Bishop Philip Anyolo of the Homa Bay Diocese at the diocese headquarters.
Governor Okoth Obado said: "I have no problem with the Catholic Church. I respect every church because I'm also a Christian.
"What we need is a lasting solution to the matter.
The two men have agreed to find a solution that is peaceful and helps build up a positive relationship between the Church and the government.
Susan Owino, Lands Board chairperson Susan Owino said: "We visited Kitere and Rapogi on a fact-finding tour and soon we shall give a verdict if the two parties cooperate."