Heads and teachers may be acting illegally because they do not know the full extent of physical and mental health problems among students, according to research commissioned by the Government.
The new report says schools staff are not following regulations in the Disability Discrimination Act and the Equality Act because they do not know how many of their pupils are disabled.
A pilot survey, carried out as part of the research, to find out how many children are disabled discovered that many teachers were unaware of mental and physical illnesses in their class - even in special schools.
The research, by academics at Bath University, says many children have difficulties which "remain invisible" to teachers. In one case it found that teachers didn't know a child had spina bifida.
While heads are not legally obliged to collect data on disability, a failure to do so, the report says, means that they are unable to ensure that they are meeting the requirements of anti-disabled discrimination legislation.
"There has been an ongoing concern about the lack of reliable data on disabled children in schools," the report says. "To date there has been no consistent way of identifying and categorising disabilities.
"The lack of this information may seriously restrict capacity at all levels of policy and practice to understand and respond to the needs of disabled children and their families in line with (legislation)."
The report says a lack of reliable data about children's disabilities is "seriously restricting" the way teachers and other experts can help pupils.
Previous research has found half of children with a disability do not have special educational needs (SEN) and half of children with SEN don't have a disability.
Around 11 per cent of children involved in the survey - 270 pupils - were identified as disabled. Half of all the 50 schools involved took action as a result of the new data.
Richard Rieser, who has trained staff in 5,000 schools on disability equality, said teachers need to improve the way they work with disabled children.
"They have difficulty identifying disabilities, even though they have a duty to do this," he said. "We don't need a new survey; teachers need to learn to ask the right questions.
"I estimate that 50 per cent of schools still don't have a disability equality scheme, and many Ofsted inspectors don't know what the regulations are."
The questionnaire was commissioned by the previous government two years ago and the researchers say their findings "confirm the importance" of gathering the information.
It is estimated there are 580,000 disabled children aged between five and 15 in the UK. Around a quarter have autism and behavioural disorders, 15 per cent have a mental handicap and 8 per cent have cerebral palsy.
Philippa Stobbs, former government SEN adviser and now principal officer of the Council for Disabled Children, said: "Many children are missing out on aspects of school life and are not able to participate fully because teachers are not thinking about their disability. They don't know the law covers illnesses such as diabetes.
"Many governors also have a notional view of disability - because they believe it's just physical, they don't think their school is affected."
All schools are supposed to have a disability equality scheme, which Ofsted inspectors have to judge teachers on.
From next spring the duty is being relaxed and schools will only have to produce a general equality statement. The former government wanted information about disability to be collected on the annual school census.
11% - Percentage of children that the survey identified as disabled.