Unlike other public schools, Eton was exempt from the Charities Act requirement to disclose accounts before recent Government rule changes to make charities more accountable.
But Dick Davison, deputy director of ISIS, said the news would have surprised few. "Eton is extremely untypical of the schools - more than 1,100 - that are charitable trusts. Most don't even own their own buildings. It would be patently absurd to base changes in legislation on the example of Eton."
In any case, he said, for every Pounds 1 a school benefited in tax under its charitable status, it gave Pounds 2 to help pupils with fees.
The Labour party said it had no plans to end the charitable status of independent schools, but it wanted them to develop stronger links with their local communities and schools.
The college, founded in 1440 by Henry VI, takes around 1,270 boys as boarders for fees of Pounds 13,400. Around a quarter of the pupils have fees subsidised by the school's charitable trust.