Whistle-blowing policies are intended to ensure problems are investigated by giving staff, pupils or parents the chance to raise concerns confidentially or anonymously, while ensuring anyone accused of wrongdoing has the chance to defend themselves.
In a Middlesex university study bullying by staff was the most frequent problem, with allegations investigated in 39 per cent of schools. Student bullying was the next most common complaint, in 18 per cent of schools.
Anne Ruff, the report's lead author, said it was not necessarily a criticism that 58 per cent of special schools had received complaints.
"It's important that people who do have concerns feel safe and secure in bringing them up. The worst thing is if they just fester away," she said.
Special schools are a model of good practice with more than half having a policy, compared to less than a quarter of mainstream schools, she said.
Ms Ruff said: "It is even more important for special schools, particularly because of the vulnerability of the pupils and because many of them are residential. Situations of physical or emotional abuse happen more often outside the classroom."
Many of the 110 non-maintained, foundation, community and independent special schools appeared to have no policy.
Only a quarter of community special schools and no foundation special schools had a whistle-blowing policy. But many community schools may rely on the policy of their local education authority. The study said there was a fear in some schools that complaints would not be confidential and that having a policy implied such problems.
Ms Ruff said: "Some of the respondents saw whistle-blowing procedures as someone cheating on them. It's seen as a kind of grassing. In fact, they can help schools be open and transparent, and help prevent legal action."