It has independent schools declaring that they won't be used as scapegoats for stagnating enrolments in Catholic schools.

The fight began when the Catholic sector released a report warning that wealthy independent schools will be overfunded by billions of dollars over the next decade under the Turnbull government's Gonski 2.0 model.

It claimed that Catholic schools and low-fee independent schools would be underfunded.

Independent Schools Victoria chief executive Michelle Green said the Catholic sector was waging an "ill-informed and divisive" campaign.

"This increasingly desperate assault risks being seen as an attempt to distract attention from deep-seated challenges confronting the Catholic school sector," Ms Green said.

"Whatever the underlying issues, independent schools refuse to be used as scapegoats."

She said enrolment growth in Catholic schools had stagnated and was being overtaken by state and independent schools.

Almost half (46 per cent) of Catholic students now attend state or independent schools, according to Ms Green.

"The intemperate and sectarian language increasingly used by [Catholic Education Commission of Victoria] chief executive Stephen Elder should not be allowed to distract us from the fact that Catholic schools are steadily losing enrolments to the independent and government sectors," she said.

She said the commission's report was invalid and misleading.

But Mr Elder hit back, saying that Catholic schools educated one-and-a-half times as many students as Victorian independent schools.

"Talk about a knee-jerk reaction from Michelle Green - we've clearly hit a raw nerve," he said.

"Instead of responding to the facts - Ms Green has thrown up a red herring about enrolments."

He said the commission was standing up for families enrolled at Catholic schools as well as those at low-fee independent schools.

The commission's report took aim at socioeconomic status (SES) scores that determine school funding - a methodology that is being reviewed by the federal government's National School Resourcing Board.

The current formula looks at where students live, but does not take into account the personal circumstances of families.

This means that it fails to recognise that high and low-fee schools in the same neighbourhood attract students from different backgrounds, according to Mr Elder. He believes this means the model unfairly favours wealthy independent schools, and short-changes poorer schools.

But Ms Green said that during the formula's 17 years of operation, not a single Catholic school had appealed the score it received.

She said the same model was used by the commission to determine how it distributed funding to its schools.

Federal Education Minister Simon Birmingham said the review of the SES score methodology would ensure that communities with the greatest needs received the most support.

It will also assess the capacity of families to contribute to the running costs of their non-government school.

"This review is in addition to the extra $3.4 billion our plan is already delivering to Catholic education authorities," he said.