It means next year the average cost for a primary student will be $1900 - including other levies and excursion fees - with fees for secondary students averaging $3000.

The Canberra and Goulburn Diocese of the Catholic Education Office confirmed primary fees would rise 3 per cent from first term, 2010, with secondary fees going up 6 per cent.

This compares with an across-the-board rise of 2 per cent in NSW.

A spokesman for the office said the cross-border discrepancy was because NSW Catholic systemic schools received greater Commonwealth and state government funding than in the ACT due to a deal which funded ACT schools on a permanently lower basis, dating back to 2001 under the Howard government.

The deal was based on socio-economic status and assumed ACT families were better off than those in NSW.

The spokesman also noted that NSW Catholic schools were currently receiving more money because they were in drought-declared areas.

The ACT increases follow identical increases introduced in first term this year.

The spokesman said the office was conscious of the need to keep costs down for families and this was the minimum rise possible.

He noted secondary school fees had increased more than primary school fees because of higher information communications technology costs, among other things.

Any families that were having trouble paying their fees should talk to their school principal.