Parents whose children attend Catholic schools in the more affluent areas of Sydney will pay higher fees than those attending schools in poorer areas, and the long-held policy of a flat tuition fee will be abandoned next year.

For the first time, there will be different fee structures for the 150 schools in the Archdiocese of Sydney. For about 35 schools in richer suburbs, fees will rise by as much as 9 per cent, while some schools in the poorest areas will have a fee reduction. Discounts for siblings will also be phased out gradually.

In a letter to parents, the executive director of Catholic schools in the Archdiocese of Sydney, Dan White, said changes to the federal government's funding model meant schools in suburbs with higher socio-economic status ratings would be expected to contribute more to their individual budgets.

"As a result of this shift in the flow of government funding, it has become clear that the current system of charging the same tuition fee to every school in the archdiocese, regardless of its location, can no longer be sustained," Dr White said.

He said the fee rises would be higher than in previous years but in line with the "typical increases in the cost of education and childcare experienced around Australia".

"However, I do appreciate that for families in some areas of Sydney, the increase in fees will be higher than parents may have expected, and may, for some, impose a strain on the family budget," Dr White wrote.

The Catholic Education Office Sydney runs 150 parish primary and regional high schools, stretching from the city to Engadine and west to Horsley Park. There are also 15 independent Catholic schools – run by religious orders who set their own fees – with about 16,000 students.

Annual fees at the Sydney schools are now set at $991 for kindergarten to year 6, rising to $2053 for years 11 and 12.

Next year, most families will pay, on average, an extra 6.5 per cent, Dr White said.

"We are a very low-cost system of schools, and while it is an increase in fees, we are trying to do it in a way that is manageable to families and will be progressively increased over time," he said.

"The Archdiocese of Sydney covers the full socio-economic spread, we go from the very marginal poor areas right through to the northern and eastern suburbs of Sydney which are quite affluent, but the vast majority of our schools fit into the middle."

Dr White said they remained committed to ensuring no child would miss out on a Catholic education because of genuine financial hardship.

"About one-quarter of schools are in the higher socio-economic area but also there are about one-quarter in the very low and in fact, compared to previous year increases, their fees will increase at a lower rate," he said.

"We are probably the first at a whole of system level that are introducing those fees and that is a result of the fact that there is a new element in the national funding model, so a number of other dioceses would have to adjust their fee structure in coming years."

A spokesman for Catholic Education Commission NSW said many of the seven regional dioceses in NSW already had differential fees,

However, Sue Walsh, relieving executive director of schools in the Parramatta diocese, said they had no plans for a differential school fee model.