But once the school's student backgrounds were taken into account, its ranking jumped to above average, NZ Initiative policy analyst Joel Hernandez said.
"We want to demonstrate that the Ministry of Education now has the opportunity to identify the high-performing schools – regardless of decile," he said.
News of a potentially more objective and data-driven ranking system could come as welcome news to parents.
Auckland parents often spend a fortune buying and renting homes in suburbs that fall within their chosen school's zone so their children can gain automatic admission.
This has seen homes in suburbs zoned for Epsom Girls Grammar School worth up to 90 per cent more than equivalent homes elsewhere, the NZ Initiative report said.
Wealthier families can also spend up to $100,000 over five years on fees at the nation's most exclusive private schools.
Yet without objective data, parents were making these important decisions based on anecdotal evidence, decile ratings and "flawed" school ranking tables, the report said.
Even when low-decile schools - those with a greater percentage of students from low-socio-economic backgrounds - received high-achieving status from the Education Review Office, parents often still bypassed them, the report said.
They then typically enrolled their children in average-performing higher decile schools, it said.
In another example in the report, a wealthy school - identified only as School C - typically ranked above average for its Year 13 students' NCEA scores and for how many went on to study at university.
Yet when its students' family backgrounds were taken into account, it ranked average in both areas.
In other words, the school achieved what was expected of it but didn't excel, the report authors said.
Southern Cross Campus principal Robin Staples hailed the NZ Initiative study as "a great step forward".
"We've been working very hard with a dedicated group of teachers and we believe we've been making great progress but often it is not acknowledged," he said.
"This report confirms that our Year 13s have been performing very well."
The data-driven analysis gave his school a new way of thinking about what was working and how to further improve, along with the chance to talk to other high-performing schools about what they were doing well.
Study authors also said the new measure could better direct Government funding and policy.
Education Minister Chris Hipkins referred questions about the study to the Ministry of Education.
Craig Jones, the ministry's deputy secretary evidence, data and knowledge, said there was no single measure that told parents and school leaders how well a school was performing.
"For that reason, we are always interested in new ways of understanding school performance.
"We think there is merit in schools looking closely at the NZI measure. Providing schools with access to the information collated by NZI would require the consent of schools to extract their data from the Statistics NZ Integrated Data Infrastructure.
"We are not currently working toward this outcome but we will be interested in gauging schools' reactions to the NZI release to see if they would find value in the measure."
The report comes as school funding is already set for its biggest shake-up in a generation with a new "equity index" to replace the current decile system from 2021 or 2022.
Hipkins earlier said the new system - which had been agreed to in principle - would allocate more funds to children with so-called risk factors.
These factors would be calculated by an "equity index" based on how much time a child had been supported by public benefits since birth, whether they had an Oranga Tamariki notification or Youth Justice referral, their mother's age at birth, ethnicity, and father's offending history.
