The majority of secondary schools in the South Tyrone and Fermanagh area have slipped into the red, racking up debts of £2,076,926, according to the latest figures from the Department of Education.
A total of eight local secondary schools have a budget deficit, while six are in surplus.
The combined total of the shortfall is the second highest for any constituencey area in Northern Ireland.
Heads and teachers have been complaining about deepening problems with funding shortages - with warnings they might have to cut staff and services.
Earlier this year, education leaders delivered a shock warning that an unprecedented budget crisis could even lead to shorter school days and less subjects for pupils.
Groups representing post primary schools in the voluntary grammar, controlled and Catholic sectors have demanded that Stormont steps in to prevent a generation of children having their educational opportunities limited.
They have warned that the crisis will lead to a reduction in subject choices at GCSE and A-Level; inability of schools to deliver the statutory Entitlement Curriculum; larger class sizes; a potentially shorter school day; an increase in non-specialist teachers delivering the curriculum; and reduced educational opportunities for a generation of pupils
The Department of Education is facing a cash reduction of £72m in its resource budget in 2016/17, and in March former Education Minister John O’Dowd announced the Aggregated Schools Budget will be cut by 0.8%.
On top of absorbing this cut schools must also fund a 3.4% rise in employer National Insurance contributions - an average £70,000 increase per school - as well as a 4.1% rise in employer superannuation contributions and cost of living pay rises for staff of between 1% and 2.2%.
A spokeswoman for the Department of Education said that the minister had protected the Aggregated Schools Budget as far as possible.