The warning comes in a letter from the finance director at the Department of Education (DE), Gary Fair.
Mr Fair said that the department was not in a position to confirm individual school budgets for 2017/18 yet.
However, he said schools would need to make "difficult decisions" in advance of the start of the new financial year.
The letter, sent on 15 March, is addressed to chairs of boards of governors of all schools.
Mr Fair said that as a 2017/18 budget was not agreed before the assembly was dissolved, school budgets cannot be finalised.
However, he said that DE, like other departments, had to "plan for a level of reductions to inform their spending plans in the initial months of the year".
"In light of this, the Department of Finance has advised that departments should plan on the basis of potential reduction scenarios of 2%, 4% and 6%," he added.
Indicative or provisional budgets for each school have been placed on DE's website, but Mr Fair said these were for planning purposes only.
"The budget outcome for your school in 2017/18 will only be known following discussions taken by the incoming administration," he writes.
"There is likely to be an extremely challenging budget position in 2017/18.
"It is therefore essential that you identify those areas of spend that can be deferred until there is more certainty over the budget position and the scale of any reductions required.
"While I fully appreciate the difficulties surrounding the financial position facing the education sector, I regret that I cannot provide any more certainty about 2017/18 budgets at this stage."
Schools have been told that they face "an extremely challenging budgetary position in 2017-18".