The Education Authority (EA) has refused to approve the budget plans submitted by 632 schools, the BBC has learned.
The authority said it was because those schools were unable to show they could stay within their allocated budgets in 2017/18.
By contrast, only 239 schools have had their spending plans approved.
If the EA does not approve a school's budget plan, it can take more control over the school's financial planning.
School principals have had to submit three-year spending plans, covering the years 2017-2020 to the EA.
'Significant financial pressure'
For the 632 schools whose plans have been rejected, this means they do not yet have approval to spend the money they say they need to spend to run the school.
In letters to each of the schools affected, the EA said it would "work with you throughout this financial year to address the issues reflected in your school's plan."
EA Chief Executive Gavin Boyd said the body's budgets were tight:
"The problem is that so many of our schools are under such financial pressure, that if they all overspent by 5% in year then the budget for the system as a whole would be 5% over and we simply don't have the resources," he told the BBC's Evening Extra programme.
Mr Boyd said there were two possible solutions to the financial problem: a large injection of money or a "fundamental transformation" of the the education system.
However, he said that transformation could not be achieved in the short term.
Earlier, an EA spokesperson told the BBC that the education sector was facing "significant financial pressure".
"Six-hundred-and-thirty-two schools have not yet had their plans approved as they were unable to demonstrate they could live within their budget allocations for 2017/18," they said.
"EA continues to work with these schools to help them develop plans which demonstrate they can live within their budgets.
"We continue to highlight the increasing financial challenges facing the education sector and the growing demand for services as we move into 2018/19 and beyond."