The system is set to be streamlined from its current three-tier hierarchy of secondary, middle and lower schools to just secondary and primary schools.
Anna Woods, whose child is due to go to Ecton Brook School, said: "Everybody is shocked. The children are traumatised and the parents are devastated."
"It'll end up coming out of the taxpayers pockets."
Hina Raichura's daughter Krishna, 10, goes to Boothville Middle School.
She said: "We don't know what is going to happen.
"You have it in your head that they will move at a certain stage of schooling but where will the children of Boothville go?
"We need to know more because it is our children's education."
Staff upheaval
Northamptonshire County Council said the children would not face major disruption.
The chairwoman of the council's education committee, Olwyn Loud, said: "This will be an upheaval for staff but hopefully not so much for children".
"The education achievement in Northampton is significantly below what it should be and after spending a lot of time and effort, we have concluded the three-tier system is the problem.
"The system has had its day. Nobody is being trained to be a middle school teacher anymore, he said.
"We are carrying out a skills audit among staff asking what sector they would prefer to work in and there will be staff development and retraining."
'Radical' plans
Middle school teachers say they face an uncertain future.
Moray Gompertz, head teacher of the All Saints Middle School - which would become a primary under the plan - said: "This scheme seems to stick the knife into middle schools".
"In my school, there will be a staff of 20 instead of 27.
"We have known about the plans to do away with the three-tier system for some time but nobody in their wildest dreams thought it would be as radical as this."
The scheme is due to be phased in by Northamptonshire County Council over a three to four-year period.
A similar scheme is causing controversy in Wiltshire where a meeting is due to be held to discuss the proposals.