The report said charter schools look at the NCEA pass rate of students at each NCEA level who left school and the schooling system - for example school leavers who achieve NCEA level one, where as state schools used the recommended Education Count figures which are reported as 'leavers achieving NCEA level one and above'.
When the Education Counts figures, which are publically available online for all schools, were applied to Te Kura Hourua o Whangarei Terenga Paraoa, it did not meet targets in 2014.
But Raewyn Tipene, chief executive of the He Puna Marama Trust which runs the charter school, said NCEA pass rates from NZQA told a different story.
"I absolutely refute Hipkins' statements that our NCEA standards results are overstated. They are higher than the average school ... I am absolutely disgusted that he rubbished the efforts of our teachers and our Maori students purely for political mileage," she said.
NZQA 2015 roll-based pass rates for the school show 80 percent of Year 11 students achieved NCEA level one compared with 74.4 per cent nationally; 92.9 per cent of students achieved NCEA level two compared with 76.4 per cent nationally; 71.4 per cent of students achieved NCEA level three compared with 63.7 per cent nationally and 71.4 per cent achieved university entrance compared with 62.7 per cent nationally.
Roll-based pass rates capture all students on the roll for each year level, whether they participated in NCEA or not.
ACT Party leader and education under-secretary, David Seymour, said Labour was "cherry-picking" the measure that best suited its "union driven agenda".
Mr Seymour acknowledged there were flaws with the leaver base being measured, as they didn't capture students who remained in school, and said partnership schools were held to account through contracts which use both roll-based and leaver-based standards.