The annual survey by law firm Browne Jacobson, run in conjunction with the Association of School and College Leaders, shows that 68 per cent of school leaders are unhappy with the new funding system for SEN.
Furthermore, 84 per cent are unhappy with the notional SEN budgets that they have been allocated.
Almost 500 school leaders took part in the study, with more than half being from secondary schools.
A total of 76 per cent of the secondary leaders said they are expecting to have to use funds from their overall budgets to supplement the notional SEN budget, while 91 per cent of primary schools said they would have to divert funds too.
Only seven per cent of both the secondary and primary leaders in the survey said they would not be dipping into their overall budget for this purpose.
The new system, introduced last year, means that on top of the basic per-pupil funding, schools are expected to meet up to £6,000 of the extra costs for children with SEN before the local authority takes up funding out of the High Needs Pupil Block.
Elsewhere in the survey, half of the secondary school leaders said they were “very dissatisfied” with the government’s funding of education generally.
And as a result of financial pressures, 71 per cent of the secondary school leaders said that reducing costs is a “major priority” this academic year.
A quarter of the secondary school leaders said they would be looking to re-direct funds from back office to frontline services. Furthermore, 35 per cent of both the primary and secondary leaders said they were considering “staff restructuring programmes”.
When it comes to staff morale, 37 per cent of the secondary leaders said it had worsened in the past 12 months, while another 37 per cent said it was roughly the same.
Notably, 42 per cent of all the school leaders said that the introduction of performance-related pay had had a negative affect on morale, with 50 per cent reporting that it had led to no real change in morale.
Nick MacKenzie, education partner at Browne Jacobson and author of survey, said: “The growing financial pressure placed on the shoulders of thousands of school leaders up and down the country is palpable, leading to an environment of growing uncertainty and falling morale.
“The decision not to proceed with a fairer national funding formula for schools for the time being will have only added to the growing frustration felt by many school leaders.
“In addition to the government’s funding policy there will be employer contribution increases to the Teachers’ Pension Scheme next September, followed in 2016 by changes to National Insurance contributions which will heap more pressure on squeezed budgets.
“However, it is clear that dissatisfaction among school leaders extends well beyond school budgets. The deep concerns expressed by school leaders in delivering the new SEN framework and assessments should also act as a further wake-up call.”