More than 60 schools are losing vital funding which allows them to run initiatives such as breakfast clubs and after-school activities.
There is set to be a major rejig in terms of which schools benefit from the £9m extended schools budget in the 2018/19 financial year.
Some 63 schools will lose out next year after being found to no longer qualify for the funding, including Lumen Christi College, Foyle College and Glastry College on the outskirts of Newtownards.
Our Lady Queen of Peace Primary School in Dunmurry has been a long-term recipient of the funding, but is now set to lose the £17,500 it receives under the scheme.
Its principal Cathal O'Doherty said it's the latest in a series of cuts which are crippling his ability to run the school.
"It is cut after cut after cut," he told the Belfast Telegraph.
"Schools have become experts at working to manage each and every cut, but it is getting to the stage where they can no longer be absorbed.
"We are now losing £17,500. We have got a buffer of £4,000 to get us through until June.
"The school is oversubscribed so our demographic has not changed."
Mr O'Doherty said he hopes to retain the school's breakfast club, but emphasised how challenging that is going to be.
"We will try to keep that going, but the clubs will have to become self-sustaining, we will have to fundraise to keep it going," he said.
He has been principal at the school for three years and says he has seen a number of cuts in that period.
He claimed the school is down by £54 per head overall from the same time last year.
SDLP councillor Brian Heading said: "In the last few months, three cuts in education funding have been announced.
"A cut of £54 per child in every school, a review into Special Education and now changes in the extended schools funding.
"This is education by the balance sheet and accountancy, not by building and improving the life chances of the next generation. This loss of funding will place further pressure on school budgets, teachers and families."
Mr Heading continued: "Those in charge of the Department of Finance need to ensure that education is treated as an essential public service, and that this is reflected in its budget."
A spokesperson for the Department of Education said around 500 schools with a high proportion of disadvantaged pupils across Northern Ireland will benefit from more than £9million via the Extended Schools (ES) programme in the 2018/19 financial year.
"Participation in the ES programme, as well as the allocations due, are assessed on a yearly basis and will vary from year to year according to an analysis of pupil enrolment data for individual schools gathered through the annual school census exercise," he said.
The spokesperson said that qualifying thresholds for the ES programme had been changed to use the new updated Northern Ireland Multiple Deprivation Measure (NIMDM) replacing 2010 rankings.
"This has had an impact on some previously qualifying extended schools in that they no longer meet the criteria for funding and will have to exit the programme in 2018/19, whereas some schools not previously in receipt of ES funding are now entitled to receive such support this year.
"Altogether, 63 schools which participated in 2017/18 have been assessed as not meeting either the area-based or FSME (Free School Meal Entitlement) qualifying criteria in 2018/19 and will therefore exit the programme this year."
The spokesperson said that 43 new schools are now fully eligible and a further 25 schools which had been in the programme but fall just short of the 2018/19 threshold are being given a "buffer zone" which will allow them to continue participating, receiving a reduced (50%) allocation for a period of one year.