Dozens of schools are yet to receive 'shared education' cash due to a stand-off over controversial pupil assessments.
About 7,000 members of the Irish National Teachers' Organisation (Into) are involved in industrial action short of strike.
This includes a refusal to recognise assessment arrangements they claim have "no value to pupils, parents or teachers and is distracting from the real education of pupils".
Principals were warned that full compliance with end of key stage `levels of progression' was a mandatory condition of shared education funding.
The £25m Delivering Social Change Shared Education signature project is designed to create "a more cohesive education system" in which children from different community backgrounds can be educated together.
A call for applications targeted up to 600 schools that could demonstrate a significant commitment to shared education.
Those whose applications were approved received letters from the Education Authority (EA) telling them how much money they would receive, subject to terms and conditions.
They must agree to regular monitoring arrangements, which rely on pupil outcomes at the end of Key Stages 2 and 3, using the levels of progression.
The EA letter reads: "Full compliance with the statutory assessment process is, therefore, a mandatory condition of the funding."
This angered unions who have, for the past two years, been boycotting the arrangements.
The EA said to date, 55 schools demonstrated they met all of the criteria, including compliance with the statutory assessment process.
"These schools can now access the relevant funding," a spokeswoman said.
Into northern secretary Gerry Murphy said members are unhappy because dozens of schools are being denied funds.
"Conditions were only added after the applications had been accepted," he said.
"There are considerable amounts of money at stake here and in a situation where schools are facing cuts, I think it is a cynical exercise by the department in attempting to break this action. It also calls into question the department's commitment to shared education."
A department spokeswoman said the aims of the project were to improve educational - including reconciliation - outcomes resulting from schools working collaboratively on a cross-community basis.
This was endorsed by the findings of the assembly education committee's inquiry on shared and integrated education this week, she added.
"Amongst the committee's recommendations is that shared education be defined as curriculum-based interactions that always foreground educational improvement and for consideration to be given to objective impact measures based on educational improvement in the first instance and societal reconciliation in the second," she said.
"The statutory assessment arrangements offer a common framework for the assessment of core skills across the school system, and are the only adequate means of reporting attainment against the cross-curricular skills as key educational outcomes defined in the curriculum.
"Consequently full engagement with the statutory assessment process is necessary in order to evaluate the success of the programme at school and system level. It would not be defensible to suggest that schools could participate in a programme aimed at improving key-stage outcomes without assessing or reporting those outcomes."
