Teacher and principal groups say the gap between schools in rich areas and those in poor areas is growing and Government funding for poorer schools must increase.
Schools in poor communities dominate the Auditor-General's list of schools in serious financial difficulty.
The list of 31 schools includes 25 which are in the bottom half of the decile ranking of socio-economic status.
Ten are decile one schools and ten others are in deciles two and three.
Only two are decile 10.
The Secondary Principals Association, the Post-Primary Teachers Association and the primary school teachers' union, the Educational Institute, say such schools are finding it increasingly difficult to make ends meet.
They say extra Government funding for schools in poor communities is not enough and the gap between rich and poor is growing.
But the Ministry of Education says the number of lower-decile schools in serious trouble is too small for meaningful comment on trends.
It says 97% of them are not in serious difficulty.
The Office of the Auditor General provided the list on Thursday following the publication of a summary of audits of school financial statements on Wednesday.
Nineteen were listed as being in serious financial difficulty last year.