Schools identified 11.7 per cent of pupils as having special needs, with 1 per cent being statemented.
The figures are lower than those in the state sector - where 1.7 per cent of pupils in mainstream schools are statemented, and 18-20 per cent have special needs.
The largest category of special need in the independent sector was dyslexia, making up 43.4 per cent of the total. Other learning difficulties contributed 10.7 per cent.
The survey findings - based on returns from 547 schools - were published this week by the Independent Schools Council, alongside its first SEN guide for heads.
Alistair Cooke, the ISC's general secretary, said the guide was intended to counter the impression that "independent schools, as a collection of elite establishments, are not interested in special needs".
Headteachers at the guide's launch reported regional variations in the amount of local authority support for their SEN pupils.
One head said that her local authority - Birmingham - paid for 12 hours of classroom assistant time to support a pupil with autistic tendencies.
But another, in Bedford, received no state funding for his statemented pupils. Instead, parents were charged pound;18 an hour for extra one-to-one tuition - on top of the school's standard fee.
The Government is proposing to amend the SEN code of practice to make it clearer to education authorities that they can share the costs of independent-school placements with parents.
'SEN in Mainstream Schools - a head's guide' is available from Learning Works Int Ltd, on 01672 512914.