The church in a statement took a "strong exception" to the directive by the GES order stating that it "cannot accede to the unilateral directive issued by the Ghana Education Service."
It said the GES "respects the long-standing partnership between Government and Mission Schools."
It argued that the school rule in question "is a long-standing one which is also non-religious and various renowned Muslim ladies in Ghana have passed through the school adhering to such a rule."
The GES earlier directed Wesley Girls High School to allow a Muslim student to fast.
Reports stated that a student was denied the right to fast in the ongoing Ramadan is disturbing.
In a statement, the GES directed all schools to allow Muslim students to fast.
It, however, asked parents to sign an undertaking that they will not hold the schools responsible for any adverse health implication as a result of the fasting.
"Fasting undertaken by students for various reasons and observed differently by the respective groupings have had varied health implications on our students over the years.
"The net effect was that students developed various health conditions. The school, therefore, took the decision then that irrespective of one’s religious background, fasting was not permitted," it added.