The four remaining charter schools which opened in 2014 have all been paid a performance bonus despite three not meeting their targets.
Documents released to the Labour Party under the Official Information Act show that Education Minister Hekia Parata approved the payments - 1 per cent of the school's budget - on advice from the Education Ministry and Charter School Authorisation Board.
The payments total around $60,000 and were made to Vanguard Military School, Terenga Paraoa, the Rise UP Academy and South Auckland Middle School.
The school at Whangaruru did not receive a payment, as it was closed down for performance reasons.
Labour education spokesman Chris Hipkins said only two out of four of the schools met their contracted targets, while another one had a compliance issue.
"Documents obtained by Labour under the Official Information Act show Education Minister Hekia Parata was advised that three of the four schools had failed to meet all their obligations, but she gave them bonuses anyway," he said.
He said the Government was "shovelling money" at charter schools while state schools were under increased strain.
Act Party leader David Seymour said the payments were not "bonuses" but part of their normal funding that had been withheld.
"Chris Hipkins does not even understand what a bonus is yet hysterically attacks Partnership Schools at every opportunity."
The documents show the areas of non-compliance were roll numbers and student engagement. Vanguard Military School didn't meet its minimum roll requirements, but said that was because some students left after achieving NCEA early.
It also didn't meet engagement targets - having too many suspensions and expulsions - but said as it was a military school it had a hard line policy on behaviour.
South Auckland Middle School also didn't meet engagement targets, but did not explain why.
Terenga Paraoa had not complied with a well-being survey, which was also required.
All the schools' achievement targets appeared to have been met, the documents said, but there was limited performance data. It said it was difficult to draw definitive conclusions after only one year.
There are now eight charter schools in operation in New Zealand. The second tranche of four schools opened in 2015, and another two are expected to open next year.
Charter schools were introduced as part of Act's confidence and supply agreement with National. Officially called "partnership" schools, they are privately run and publicly funded.
Education minister Hekia Parata was in Estonia and not able to comment.