Boarding schools will have to spend thousands of pounds for health and welfare inspections to help meet new national standards.

National boarding standards for the inspections, to be undertaken by the National Care Standards Commission, are being introduced after consultation with the independent sector. However, say schools, amicable discussions with the Government have been soured by the imposition of hefty inspection fees.

The largest boarding schools, such as Eton, face fees of around pound;9,000 a year for the inspections, while a typical charge for a school with 600 pupils might be pound;5,000. The average termly boarding fee is pound;4,736, according to the BSA. Schools will be inspected once every three years.

Adrian Underwood, director of the Boarding Schools Association, said: “It is not the principle of charges we object to, but we feel the level is too high. We think half that would be reasonable.”

The standards will be administered by the commission, which takes over welfare inspection of boarding schools in April this year. Previously such work had been the responsibility of local social services.

The Department of Health said boarding schools had been given one of the lowest regulatory fees because they would be inspected less frequently than other organisations.

A department spokeswoman said: “Ministers made it clear that the fee policy for all sectors would be to recover the full costs of the commission. The fee payments will bring boarding schools into line with the fee policy for all other welfare inspections of social care and independent health care services.”

But Mr Underwood vowed to fight the charges, saying: “We are still in consultation with the Department of Health, but we have widened the consultation to Education Secretary Estelle Morris and the Cabinet Office education department. We have not got a definite reduction yet but we are hopeful.”

* England’s smallest private schools face paying thousands of pounds to be inspected by the Office for Standards in Education.

A total of 1,200 private schools - accounting for 85 per cen tof pupils - are affiliated to the Independent Schools Council and are scrutinised by its inspectors.

However, 1,000 others are now expected to be charged between pound;2,000 and pound;10,000 for inspections. Many of these have fewer than 100 pupils.

The Government has mooted a sliding scale, based on the number of pupils, with fees of between pound;2,000 and pound;10,000.

However, the consultation did result in new schools being let off charges of up to pound;5,000 for “pre-registration” inspections.