A report by the charity says that one in 110 children have autism. Yet more than 70 per cent of schools are unsatisfied with teacher training for the condition. Less than a third of parents of autistic children in mainstream education are satisfied with the understanding of the condition at their school. And one in four was dissatisfied with the understanding of it among special educational needs co-ordinators.
The society said lack of training meant many staff were unable to adapt their lessons and materials to suit pupils with autism. This could be one reason why a quarter of such pupils are excluded.
It wants the Government to fund, develop and distribute resource packs on autism for staff and to ensure all Sencos are trained in the condition.
Jenny Ravenhill, the society's principal psychologist, said cuts in in-service training for teachers had worsened the situation.
"The help and support that teachers need isn't there," she said.
The Make school make sense for me report, which contains interviews with 28 children, will be published on Wednesday and will be presented to Professor Sir Al Aynsley-Green, the children's commissioner.
Asked what a good teacher would be like "Hugh", 14, said: "Helpful not impatient, they'd understand me and always get the full picture of what's going on."
Another pupil with autism, in his first year at mainstream secondary, said he had problems because most teachers did not write instructions on the board. "It's easier when they write it down," he said. "Then I can just look up at the board and see I what I have to do."
"David", 12, also at a mainstream secondary said: "Sometimes I have to walk out of lessons. When I am stressed I have to go away but unfortunately there isn't anywhere to go."
The Training and Development Agency for schools said there was no specific mention of autism in standards for teacher training providers, but trainees had to understand their responsibilities for special educational needs.
Joshua Muggleton 16, was displaying Asperger's Syndrome symptoms and had become clinically depressed by the age of 11.
"I was just getting so wound up and so mentally tired," he said. "I took practically every antidepressant I could stomach until we fell onto one that worked. However, that did not tackle the problem of school."
By the time he was diagnosed in Year 10 the situation was unmanageable. "I just got to a point where school had become a phobia and I could not get out of the car," he said.
"As soon as I got in the car to go to school, I'd start having a panic attack."
He describes the day a mental health team signed him off school as the happiest of his life and says he still has nightmares about his experiences there.
Jenny Ravenhill's advice for dealing with autism
* Don't sit pupils near a window. They need calming, stable settings to avoid distraction
* Keep language short, simple and to the point
* Wherever possible support verbal instructions with something visual that pupils can refer back to
* Find out what keeps a child calm and happy and let them use it. For example headphones or dark glasses to filter out distractions
* Every child is different - learn what makes them tick so you can see the world through their eyes