The plea from the Association of Christian Teachers (ACT) comes as the government's spending watchdog warns the efficiency savings may "put educational outcomes at risk".
Director of Strategy Clive Ireson told Premier's News Hour: "It will depend on how well schools can plan and this is where governors in schools [come in].
"There are many Christians on governing bodies who we need to pray for at the moment; they will be taking these decisions.
"They won't be taken by government, they'll be taken by governing bodies of schools, on a local level."
The National Audit Office (NOA) warned on Wednesday the savings will equate to an eight per cent real terms reduction in funding per pupil by 2019-20.
It claimed the Department of Education's pursuit for efficiency savings was "clearly reasonable" but warned it remained "uncertain" how schools will be able to respond.
The NAO said: "The department believes that schools can finance high standards by making savings and operating more efficiently.
"However, it has not yet completed its work to develop tools and advice to help schools secure crucial procurement and workforce savings."
Clive Ireson from ACT added: "Pray for clarity and that clarity will come soon from government as to how this will affect schools.
"Schools can't plan on a yearly basis; they need to plan for three years and so they need some clarity now."
The Government says the savings are achievable.
Click here to listen to ACT's Clive Ireson speaking with Premier's Marcus Jones: