Church leaders welcomed the move but called for an educational partnership agreement to make a smooth transition.
Bishop John Kwofie of Sekondi-Takoradi, who is in charge of education for the bishops' conference, said the government originally helped mission schools because it was in charge of education.
"Educating the population of a country is an immense duty that the state cannot do alone," he said.
"This assistance, however, evolved into what seemed like taking over the schools from their rightful owners who have, in some instances, been relegated to the background on account of the lack of clear policies or agreement," he said.
"I think returning the mission schools to their owners is a way of recognizing the contribution religious bodies have made and the purposes for which they founded mission schools," he said, adding that it is "recognition by the government that the religious bodies are able partners in the agenda of government for a better quality of education in our country."
He said the churches expect to work with the government on a memorandum of understanding for the management of schools established by the religious bodies.