The analysis, using the most recent My School data, showed that between 2009 and 2014, combined states and federal government annual funding for independent schools rose by $1911 per student, in increase of 30.3 per cent, not adjusted for inflation.
Funding for public schools rose by $1539 per student, an increase of 14.6 per cent.
For Catholic schools, funding rose by $2332 per student, an increase of 30.2 per cent.
Ms Haythorpe said the figures highlighted the importance of implementing the full six years of Gonski funding, without which the system would regress.
"In the years leading up to Gonski we were not funding schools on the basis of need. We had a flawed and inefficient funding system, which was delivering the biggest gains to private schools," Ms Haythorpe said.
The first amounts of Gonski funding coming into the system in 2014 was "making a difference in schools – students are beginning to get the smaller classes, one-to-one support and extra literacy and numeracy programs they need".
"But without the full six years of the Gonski agreements we won't close these gaps in funding."
"Malcolm Turnbull's plan would see gaps in resources between schools grow, and fail to address the inequities caused by a system which gave the biggest funding increases to advantaged schools.
"He wants to return to a system which ignores student need and leaves thousands of students without the support they need to succeed at school.
"Disadvantaged schools don't need cuts to Gonski. They need the $4.5 billion in investment Labor and the Greens are promising, which will see all schools with the resources they need to educate their students."
The AEU analysis found that in 2014, independent and Catholic schools had more resources (recurrent funding) per student than public schools, including fees and other income, "despite educating far smaller numbers of disadvantaged students".
It found there was $17,604 annual funding per student in independent schools, $12,998 per student in Catholic schools, and $12,779 per student in public schools.
In addition, low socio-economic status students comprised 9 per cent of independent school enrolments and 14 per cent of Catholic schools', compared to 30 per cent of public school enrolments.
But Federal Education Minister Simon Birmingham said Labor and the unions were selectively using data to peddle a scare campaign. ( Well they're not actually!)
He said between 2004-05 and 2013-14 Federal funding on a per-student basis for government schools had grown in real terms by 66.1 per cent, and funding for non-government schools had grown by 18 per cent.
Public school students received "significantly more total government funding per student than what goes to private school students".
"On average, total government funding for a student going to a public school is over $16,000 per year, while the support for a student attending an non-government school is $9,300 – more than 40 per cent less."
Mr Birmingham said: "Any disparate growth in funding for non-government schools relative to government schools is entirely down to state government decisions, given federal support has been growing much faster in the government sector.
The Coalition was "the only party with a fully funded and affordable plan that ensures money is directed where it's most needed and focuses on proven measures that will improve outcomes in literacy, numeracy, STEM subjects and prepare students for the jobs of the future".