The Ulster Teachers Union, at its annual conference this weekend, is due to demand a review of the funding system to ensure that the state and maintained sectors - the latter attended nearly entirely by Catholics - benefit equally.
And it is expected to urge an investigation of the funding of schools by the Standing Advisory Commission on Human Rights, set up in the 1970s by the Government. Four years ago, it reported that Catholic schools' capital budgets had also been under-funded, although this has since been corrected. Research has shown the formula funding discrepancy can amount to as much as Pounds 85,000.
The Southern Education and Library Board has also urged the Government to examine the controversy.
The issue of formula-based school budgets has long been a bone of contention in England and Wales, where local management was first introduced.
David Allen, general secretary of UTU, the only locally-organised teachers' union in NI, said: "There is no doubt that this is happening and it is an issue which is not going to go away.
"But it is not only creating a blatant discrepancy between the two main sectors of education, it also creates unfairness within each of the sectors. Parents who are, for example, owner-occupiers are in effect subsidising children in deprived areas.
"What we want to achieve is to take the sectarianism out altogether. If the Government wants to target social deprivation, we are saying that funding for that should not come from other parts of the education budget."
The apparent anomalies arise because a small part of funding is determined by the number of pupils in a school eligible for free dinners under a Government programme to target social needs.
Since more Catholic families are likely to be on lower incomes than their Protestant counterparts, the formula is accused of discriminating against controlled schools.
This week David Blunkett, Labour's education spokesman, promised teachers' leaders in Glasgow that his party would review the funding criteria to take account of the higher teaching costs in those schools where staff turnover is low.
Southern Board chief executive Gerry Kelly said there had to be a better way to tackle social deprivation in Ulster and use public money more effectively.
UTU president Margaret Wilson told the conference in Belfast, which began last week, that the main reason education reforms had caused chaos in Northern Ireland was because the Government had refused to listen to grassroots opinion.
"The cake is being divided into too many pieces and by the time money gets to the pupils in schools the amount is insignificant," she said.