Mencap said the Government had chosen to prioritise racist and homophobic bullying over the needs of disabled children.
Dame Jo Williams, its chief executive, said: "We have not seen clear leadership in combating disablist bullying.
"Bullying results in children missing out on opportunities to learn and make friends, socialise and play, and can affect their development in adult life."
Leonard Cheshire Disability, which works with more than 20,000 disabled people, said 40 per cent of respondents to a survey said that teachers had lower expectations of disabled pupils. More than half said they had faced discrimination in education.
John Knight, head of policy and campaigns, said: "Education is absolutely critical to a person's future. So it is extremely worrying that so many disabled people had faced discrimination or prejudice.
"It is vital that education professionals are fully trained in disability issues to make sure there are equal opportunities throughout the education system."
A spokesman for the Department for Children, Schools and Families said the Government was working on guidance to help teachers tackle bullying of children with disabilities.