A survey of 1,100 school leaders found that delays to assessments, insufficient budgets and cuts to local authorities were hampering the ability to cope.
Department for Education (DfE) statistics published last year showed there were more than 1.3 million children in England - 15% of pupils - identified as having special educational needs or disabilities. Of these, 1.1 million are in mainstream schools rather than special schools.
The study by The Key, which provides leadership and management support to schools, is calling for increased funding.
82% of mainstream schools in England do not have sufficient funding and budgets to adequately provide for pupils with SEND (pupils with special needs or disabilities) 89% of school leaders believe cuts to local authority services have had a detrimental impact on the support their school receives for pupils with SEND. Three-quarters of schools have pupils who have been waiting longer than expected for assessment of special educational needs or an education, health and care plan. 88% of school leaders think initial teacher training does not adequately prepare teachers to support pupils with SEND.
The Key survey suggests primary schools are under the most strain when it comes to providing for pupils with SEND.
Eight in 10 primary school leaders said their budget was insufficient, while seven in 10 at secondary school level raised concerns about funding.
Nine in 10 at primary level have had the support they receive for SEND provision affected by cuts to their local authority, while this was the case for eight in 10 secondary leaders.
Delays in assessment of SEND and long waits for EHCPs also appear to be more common for children of primary school age.
Eight in 10 primary schools have pupils who have been waiting longer than expected, while the figure is just over six in 10 at secondary schools.
Fergal Roche, chief executive of The Key, said: "A year on from major reforms to the national system for SEND provision, these findings represent an important wake-up call from school leaders. "Schools need adequate funding and a holistic, well co-ordinated and resourced system of support behind them to provide effectively for children with SEND."
Cllr Roy Perry, chairman of the Local Government Association's children and young people board, said: "We were clear with the Department for Education at the time that implementing the SEND reforms in the Children and Families Bill was significantly underfunded by the government and this has been borne out in reality.
Our children are the future and much more should be done in relation to children with special needs, if you feel the same then don't stay silent please,