David Vanstone, chairman of the Independent Schools Association, said large schools, often with up to 2,000 pupils, failed to meet the needs of individual pupils.
Speaking at the association's annual conference in Malvern yesterday, he said: "It sounds good to take pupils from failing schools, but the proposal ignores the fact that as each new class is introduced so buildings become more crowded and facilities overstretched. Most dangerously, because additional funding cannot resolve this problem, there is a further drift away from intimacy and individual understanding that gives young pupils the confidence they need to thrive.
"Why is it that small schools are considered essential to the pastoral welfare and educational opportunity at primary level but suddenly at 11 youngsters are expected to cope in huge, soulless institutions of more than 1,000, 1,500 or even 2,000 pupils?"
Mr Vanstone is head of the 300-pupil North Cestrian grammar school, Altrincham, which charges pound;5,100 a year. He also queried government claims that it is introducing greater independence to the state sector as it creates 200 academies - state schools independent from council control - and makes it easier for schools to gain foundation status, giving governors more powers.
Mr Vanstone said: "How dare the Government try to steal the word 'independent' for foundation schools or academies when all it plans to do is release them from the stranglehold of the local authority and imprison them behind the bars of DfES edict."