The report showed Vanguard Military School on Auckland's North Shore and Te Kura Hourua O Whangarei Terenga Paraoa reported they had met their 2014 NCEA leaver targets - but when the figures were analysed, they did not.
Vanguard reported a 100 per cent pass rate for NCEA Level 2. However, when revised in line with NCEA standards it dropped to just 60 per cent. It met Level 1 standards.
At Te Kura Hourua, neither Level 1 or Level 2 NCEA standards were met once revised: Level 1 dropped from 82 per cent to 77.8 per cent, and Level 2 dropped from 80 per cent to 55.6 per cent.
Labour Education spokesperson Chris Hipkins, who obtained the documents, said they showed charter schools have been "massively overstating" their pass rates when compared with the rest of the country's schools.
"In one case a school reported a 93.3 per cent pass rate when the facts show only 6.7 per cent of leavers achieved NCEA Level 2," he said.
"It's disappointing that we're not getting apples for apples comparisons, but it's even more disturbing that many kids are leaving these schools without the qualifications the Government says every child needs."
The latest Ministry annual report data also showed charter schools' National Standards results were declining, he said.
"Last year charter schools were awarded performance bonuses for their results while state schools are staring in the face of major funding cuts next year."
Hipkins added: "It's simply not fair that students are leaving these school with minimal qualifications while charter schools receive special treatment as state schools struggle."
The Post-Primary Teachers Association said teachers would not be surprised to hear the success rates being touted by charter schools were not true.
"Charter schools are a bad idea, for a multitude of reasons, but to hear that their so-called success rates are not based on fair measures is disheartening," PPTA president Angela Roberts said.
"We question why the Government put in place a different system for measuring student success for charter schools in the first place."
Recent results in two top international studies released in the past week showed New Zealand students falling behind their international counterparts, and Roberts said this showed the need for investment in public education.
"Comparing the USA and Sweden, which have done the most to promote charter schools, and perform below New Zealand, to Singapore, Japan or Estonia, which don't have them at all and are at the top of the world, gives a pretty clear message of who we should and shouldn't be learning from," she said.
"High quality public education is a cornerstone of our society. It is innovative, successful and transparent.
"We believe government should focus on what's working, and not spend any more time or money propping up inadequate alternatives like charter schools."
