The NSW Teachers Federation-commissioned report estimates the state government will overfund private schools by around $850 million in the five-year period from 2019 to 2023.
But independent school representatives say the analysis overlooks the large share of private schools that are still underfunded through the same agreements.
The report, compiled by economist Adam Rorris, found 28 private schools had been overfunded by more than $1 million in 2021.
The largest amounts went to Barker College, William Clarke College and Oakhill College Castle Hill, which were each overfunded by more than $2 million.
Its calculations are based on Schooling Resource Standard (SRS) benchmark, used by state and federal governments to estimate the amounts of taxpayer funding each school should receive to meet their needs.
Under a transition agreement introduced in 2019, NSW private schools that were receiving more than the benchmark would have their funding gradually reduced to the standard by 2029.
Those receiving less than their entitlement would have their funding brought up to benchmark level by 2023.
The report found that nearly two-thirds of the 367 private schools included in its study were overfunded by the NSW government in 2021, while 35 per cent received the same as or less than their SRS entitlement.
Over the five-year period from 2019-2023, the private school sector, including Catholic schools, would be overfunded by $850 million, it said.
At the same time, public schools were being underfunded 10 per cent - or around $2 billion per year - based on the same benchmarks.
Some 80 per cent of independent schools' SRS entitlement is provided by the federal government while the remaining 20 per cent comes from state coffers. The shares are reversed for public schools.
NSW Teachers Federation president Angelo Gavrielatos said the most overfunded schools were the ones that needed the extra money the least.
"This funding inequity is making it harder to ensure every child gets the education they need," he said.
"A decade ago, governments agreed that there needed to be a minimum resource standard that all schools were funded to in order to meet the needs of their students and yet we still have this profound inequity."
But Association of Independent Schools of NSW chief executive Geoff Newcombe said the report neglected to highlight the more than 100 independent schools that received less than their SRS entitlement from the state government in 2021.
"The Teachers Federation knows full well that independent schools are in this situation through no fault of their own ... the goalposts moved when the government changed the funding model several years ago," he said.
Dr Newcombe said during the current transition period some independent schools would receive more funding and others less, with 30 per cent to lose significant funds annually until 2029.
A NSW Department of Education spokesman said the state government was the first to sign up to "needs-based, sector blind funding" and it remained committed to the model.
It said non-government schools would be transitioned to 20 per cent of the SRS by 2029, and in 2021 the state's contribution to the sector was 22.74 per cent - down from more than 25 per cent in 2018.
