Prime Minister John Key says the Government is free to ignore advice from officials after the Ministry of Education warned against unregistered teachers in charter schools.
The trial of charter schools is part of the post-electon deal between the ACT Party and National.
Schools will receive state funding, but not all teachers will have to be registered.
The ministry says all teachers in state, state-integrated and private schools are required by law to be registered.
It says registration is the single most important factor in ensuring quality teaching, and excluding charter schools would significantly damage the Crown's credibility.
Mr Key says the Government listens to a wide range of advice and teachers in charter schools would still need to be vetted by police.