It showed charter schools had been inflating their NCEA pass rates, he said.
But Seymour disputed that, saying all results are "publicly available and easily comparable using any measure".
However, the way that charter schools will report their results in future will change, he said.
"It was decided recently that the contracted performance standards for new partnership schools would use both leaver-based (Education Counts) and roll-based (NZQA) measures rather than the original blended measure," he said in a statement.
"Both leaver-based and roll-based measures have to be looked at in parallel to overcome the limitations of the Education Counts leaver-based measure and get a full picture of performance."
This would simplify reporting, Seymour said.
This evening Seymour hit out at Hipkins and Labour, saying they had failed to understand how NCEA performance is measured.
It was "totally untrue" that charter schools - also known as partnership schools - had been massively overstating their pass rates, he said.
"The Education Counts website publicly reports leaver-based NCEA achievement for both state and partnership schools," Seymour explained.
"NZQA publicly reports roll-based and participation-based NCEA achievement for both state and partnership schools. It is simple for anyone to compare the results.
"More importantly, Hipkins seems oblivious that there is more than one way to measure NCEA performance. Indeed, there are a range of different measures, including NZQA and what the Ministry reports on Education Counts."
Seymour was adamant that 2015 roll-based NCEA results for partnership schools were "excellent when compared to state schools".
Roll-based results show pass rates as a percentage of the whole roll, and are considered a more stringent measure compared to participation-based results, which show pass rates as a percentage of the number of students enrolled for a particular NCEA level.
Earlier, Hipkins pointed to Vanguard Military School on Auckland's North Shore, as an example of a charter school whose reported results didn't stand up to scrutiny.
Vanguard reported a 100 per cent pass rate for NCEA Level 2 in 2014, but Labour's leaked report said when revised in line with state school reporting standards the pass rate fell to 60 per cent.
However, Seymour disputed this, saying as more students graduated from the school in 2015, the figure improved to 84.5 per cent.
"Partnership schools are unique in being contracted to deliver specified education outcomes," Seymour said.
"That's why they have additional educational performance targets set out in their contracts that state schools don't have."
