Education officials at the Peterborough Diocese submitted an application to change Unity College, which is currently in special measures, into a church academy in September.
If the bid is successful, existing staff would all have to reapply for a
job at the academy and would only be employed if the "match" between their old and potentially new jobs was "sufficiently close".
Gordon White, county secretary for the NUT, said: "Staff are already feeling under pressure due to the demands being placed on them as a result of the school being in special measures.
"With the restructuring, they now have one eye on whether they will keep their jobs and whether they will be paid the same amount. In the current climate of uncertainty it will inevitably impact on morale.
"I have told the council the whole thing is a mess and they need to ditch the academy plans for the sake of the children, parents and staff. There is a real risk to the future stability of the school from all the changes.
"I suspect morale amongst the support staff is at rock bottom."
A letter was sent home with children on Tuesday on behalf of the academy sponsors – The Diocese of Peterborough, Bishop Stopford School, Moulton College and Northamptonshire County Council – explaining the consultation process and why the staff were being made to reapply for their jobs.
The letter read: "Some of these job descriptions will be almost identical to existing ones, some will be a little different, others very different.
"TUPE (A nationally agreed procedure for the staff of a maintained school which becomes an academy) lays down a matching process for existing staff between their old and potentially new jobs.
"Where the match is sufficiently close, existing staff will be re-appointed. There is a nationally-agreed process to support any who are not appointed in this way.
"We naturally hope that there will be considerable continuity of staff, and we will do what we can to assist any who are made redundant."