"For many schools this can become unaffordable. The more they pay support staff, the fewer hours they can employ them for.
"NZEI has been calling for teacher aides to be centrally funded and to be paid properly for many years and this report adds further weight to this call."
Green Party education spokeswoman Catherine Delahunty agreed a change in funding was needed. An inquiry by Parliament's Education and Science Committee into special education had highlighted the issue.
"There were so many people for whom they could not get sufficient or qualified, trained teacher-aide support because it is so badly paid. It is dependent on what schools can afford out of their operations grant."
Labour's education spokesman Chris Hipkins said the good will of teacher aides was being exploited.
"The funding model for teacher aides is all wrong. Government underfunding is forcing schools to make trade-offs."
Lisa Rodgers, the Ministry of Education's head of early learning and student achievement, said the Universities New Zealand survey measured the lifetime earnings of graduates.
"They've informed us that most of the teacher aides in their survey only worked part-time. This affects life-time earnings considerably.
"Many teacher aides also work only during term-time. Again, this affects life-time earnings. Many teacher aides have these working arrangements because they fit in with family responsibilities."
The ministry had been working closely with NZEI on support staff career paths and on remuneration structures, Ms Rodgers said.
"Schools tell us that they value the flexibility an operation grant provides. However teacher aides are not solely funded through operation grants - for example many schools receive additional funding for teacher aides funded for children under the ORS programme."
Ms Rodgers said most teacher aides were on pay grades that provided for the equivalent of an annual salary of between $35,000 and $50,000.
The Universities New Zealand research sampled 57 teacher aides, which was not enough to be statistically robust, she said.