Warnings the Turnbull government's school funding changes will force Catholic schools to hike their fees by $5000 a year have been rubbished by one of the country's largest Catholic archdioceses.

In a letter sent last week, the Archdiocese of Brisbane assured parents that next year's fees would be similar to this year and thanked the government for its "commitment to fair and equitable funding".

The stance from the Brisbane Archdiocese, which oversees 139 schools, represents a break from other Catholic sector authorities that have claimed they would have to dramatically increase fees under the new model.

"I would like to assure you that - despite what you may have seen reported in the media - there will be no major increase in school fees in our Brisbane Catholic Education schools for 2018," executive director of Brisbane Catholic Education Pam Betts wrote.

"I can assure that next year's fees will be similar to this year's, with a projected increase of somewhere around the 3 per cent mark, in line with the increase in our operating costs."

Federal funding for Catholic schools in NSW and Victoria would grow at a similar level to Queensland under the new funding model.

Dan White, executive director of Sydney Catholic Schools, said fee increases at the 149 schools in the Sydney Archdiocese would remain at "normal levels" next year under the government's changes.

But he said there could be "significant" fees increases in coming years for parents with children enrolled in Catholic schools in mid-to-high income Sydney suburbs.

In a letter to Catholic school parents earlier this month Dr White said: "In 2018, there will not be an increase in school fees apart from the normal annual increases that reflect the costs of running a school ... We will do everything in our power to minimise the potential increase in school fees in the long-term."

Stephen Elder, executive director of the Catholic Education Commission of Victoria, said: "The school funding model expects parents in non-government schools to pay fees.

"The Turnbull government's changes to [the] funding model will trigger significant increases in fee expectations in many Catholic schools."

Earlier this month The Australian newspaper published modelling, attributed to the National Catholic Education Commission, claiming 20 schools around the country would increase their fees by $5000 and $6000 a year from 2018 under the government's changes.

It was claimed Catholic primary schools in areas such as Balmain and Malvern East would have to raise their fees by $6000 from 2018.

In her letter Ms Betts wrote: "Next year, Brisbane Catholic Education, as a system of schools, will receive a federal funding increase which we currently estimate to be around 3 per cent.

"We will receive an increase in government funding, not a reduction.

"We thank the Federal government for its continuing support and for its commitment to providing fair and equitable funding over the next decade."

A spokesman said the letter was written to quell the concerns of parents who said they would have to pull their children out of school if fees increased by the published levels.

Ms Betts wrote she does believe the government's changes disadvantage Catholic schools compared to public and private schools.

Education Minister Simon Birmingham said: "While there have been many wild claims in this debate this letter certainly focuses on the facts and that is funding for Catholic schools across the country is increasing by 3.7 per cent every year.

"School organisations owe it to their families to tell the truth and to be transparent about any fee increase claims and with increasing funding there is no reason I can see for fee increases in the Catholic system beyond normal inflation adjustment."

Funding for Catholic schools in NSW would increase by 3.8 per cent over the next four years under the government's changes, 3.7 per cent in Queensland and 3.5 per cent in Victoria.

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