Kilmaine Primary School in Bangor has a surplus on its budget but faces a cut of Pounds 100,000 in the financial year beginning this week. The principal, Raymond Boyd, expects to lose six of his 35 teachers.
With 850 pupils expected on the rolls next year, the number of pupils per teacher will rise from around 24 to 29.
"For a minister to rob this money from education for security is pretty immoral," Mr Boyd said.
"Education is one thing this country has going for it, but now it is being decimated for reasons outside our control."
Brownlee Primary School in Lisburn is losing one of its five teachers, pushing the pupil-teacher ratio in the 120-pupil school from 24 to 30.
But even this will not make good the shortfall of Pounds 34,000, and Brownlee faces the prospect of cutting another teacher in a year's time, pushing the pupil-teacher ratio to 40.
"The board of governors was very reluctant to make any cuts," said the principal James Kerr. "We will not get back into surplus next year but we hope to do it in two years' time. Children are being punished. I have been teaching for 35 years and this is the worst I have ever encountered."