Mr Wilkinson said around 270 submissions being collated by the Ministry of Education for the Canterbury Earthquake Authority will be included in a recovery plan to go before Cabinet by Christmas.
He said there was a willingness from Canterbury schools to be more collaborative and cooperative in the future.
"You wouldn't think that the charter school concept would lead to cooperation, especially if you have performance pay for teachers."
Mr Wilkinson said it was not fair to trial charter schools on disadvantaged children in eastern and central Christchurch, particularly in the wake of the earthquakes.
"If the trial works, I suppose that's great. If the trial didn't work, then we've got poor kids.
"I think that Christchurch has had enough uncertainty in the last 18 months and for the schools in the central and eastern areas that they talk about in this document, this is just another layer of uncertainty in their future.
"I'm unaware of any schools having been approached by the Act Party or anybody else saying 'we'd like to make you into a charter school'.
"I would have expected them to have signalled that by now."
Canterbury Primary Principals' Association president John Bangma agreed.
"It's just adding more uncertainty - we've had a year of uncertainty in Christchurch.
Mr Bangma was also disappointed with the lack of consultation with the sector.
"I just think they have enough to contend with, their buildings back up, getting everything back to some form of normality ... add this complication on top of it, I really feel for those schools in that area."
Mr Bangma wanted to see evidence the charter schools would work.
"We've got a world recognised stunning New Zealand curriculum that is the envy of just about every country in the world, we're going to now perhaps let schools not even teach that curriculum. I've got concerns about these schools to employ untrained teachers. Would will allow that in the health sector?
"I worry about taking on yet another international failed system ... I don't get what the intent is. Is the intent to try to assist kids, or to save money? If the intent is to assist children, couldn't that be done by getting a whole lot more resources for state schools?"
Mr Wilkinson said it was "not democratic" that the issue wasn't put to voters before the election.
"It is a concern that the Government does a deal with a party that has got one seat in Parliament, a very small percentage of the population's party vote, and they are prepared to tip the system upside down.
"It's not a minor change."
Mr Wilkinson doubted charter schools would lift the achievements of students.
"It's not a simple matter of saying [that] paying teachers according to performance, choosing your own curriculum, raising your own revenue, etc, will do that. If the funding that was put into these organisations was put into the current state system ... I'm sure the state schools could do equally as well as charter schools."
Mr Wilkinson said the success of students has to be addressed by other sectors, not just education.
"Schools can't do it alone."