Many charter schools will be able to integrate into the state system once their contracts are terminated by the government, Education Minister Chris Hipkins says.
The government has introduced a bill to Parliament that stops the creation of new charter schools but allows the 11 existing schools to continue while they discuss options with the ministry.
Mr Hipkins announced yesterday the ministry would negotiate on a case-by-case basis with the schools as it moves to shut down the schools.
He said the government wanted to move quickly to do so, and they could be all closed by the end of the year.
Mr Hipkins told Morning Report the 11 privately owned, publicly funded schools could apply to become a different type of school, and each needed to discuss its future with the Education Ministry.
He said charter schools had been an ideological experiment and a distraction from the core mission of a publicly-funded education system for all.
"I'm not saying necessarily that those schools will close or will cease to operate," he said.
"There are some legal technicalities, there is some negotiation to go through and we're dealing with that on a case-by-case basis in good faith, as we've said from the very beginning."
He said some of them could become 'special character' schools, but they would fall into the public education system.
"So it removes the elements of concern that we have about the charter school model.
"We were concerned about the ideological underpinnings of the charter school model, it's very much a privatised education system model, whereas those other systems that I just mentioned - except for private schools - are part of the public education system."
Mr Hipkins said some of the claims made about charter schools by their supporters did not bear scrutiny, but getting into a public debate about it would not show good faith.
"What we've seen from the first charter schools that have been established is that they're not doing very much that they couldn't' do within the state school or public school system.
He said some of his government colleagues who had spoken positively about charter schools in the past were "not fans of the charter schools model, they were fans of those particular schools".
However, the government's plan to introduce the bill came as a surprise to some of the groups that run the privately-owned, publicly-funded institutions.
The operators of Vanguard Military School in Auckland had already arranged to meet with the Ministry of Education next week to discuss their school's future, and were blindsided by yesterday's announcement from the Minister Chris Hipkins.
The academy's chief executive, Nick Hyde, said he had been set to meet officials next Tuesday to discuss the school's future, and they had no warning the announcement was coming.
"I would've thought that in good faith you would pop a phone call to someone and say 'hey look, we're just going to announce this', maybe give us time to contact our parents and recruits," he said.
"I mean this morning I will be sending an email to all our parents explaining the situation and I'll be speaking to an assembly of our kids.
Mr Hyde said the school, which has 200 recruits and a waiting list, achieves 95 percent success in NCEA.