Latest figures from the Assembly government say heads have pound;18 less for every pupil in Wales to save for a rainy day or pump into major investments, such as new ICT suites, than in 2005.
Primary school reserves have been worst hit, with 178 now in the red as they struggle to prepare for the introduction of the play-led foundation phase. Forty-four secondaries, four nurseries and seven special schools are also in minus figures, fuelling fears that the cost of educational reform is beginning to bite hard all round.
However, schools in Wales on average are still sitting on a mountain of cash amounting to pound;68 million by the end of March 31 this year - equal to pound;146 per pupil.
Schools are permitted to hold reserves for contingencies. Heads have justified holding on to cash over the past few years to fund a raft of costly initiatives. They also say the way the figures are collected by the Assembly government in March does not give a fair breakdown of the actual money spent by schools over a financial year.
Gareth Jones, secretary of the Association of School and College Leaders Cymru, said: "These figures do not take into account all spending over a full year. The 14-19 learning pathways and its requirements will stretch secondary school budgets."
But this attitude has angered some teaching unions, including the NASUWT Cymru, which says schools are their own worst enemies if they hold on to cash while making teaching staff redundant.
And 22 per cent of schools are shown to have whopping reserves of 10 per cent or more - twice the recommended level of the Wales Audit Office in the latest round-up.
The Wales average for 2007 for reserves was 4 per cent, a drop of 0.4 per cent on the previous year.
Last year, strengthened guidance for local authorities in clawing back excess committed funds was published by the Assembly government
"Unless balances are being held to fund provision, schools tie up resources given to benefit pupils," said a spokesperson.
Cash reserves in March last year amounted to pound;72m, a fall of pound;12 per pupil, or 8 per cent, on the previous year. Since 2005, the percentage has fallen by 13 per cent.
The local authority with the lowest reserves left this year was Monmouthshire at pound;62 per pupil.
Top 10 best-saving local authorities per pupil in 2007
Isle of Anglesey: pound;268
Merthyr Tydfil: pound;196
Neath Port Talbot: pound;173
Blaenau Gwent: pound;157.