A school principal has called on the Department of Education to make extra places available after dozens of Year 7 pupils were turned down.
Matthew Pitts, the principal of Bangor Academy, has stated that "it is not a school decision".
The school said it had requested extra places on two occasions.
Year 7 pupils across Northern Ireland received letters at the weekend informing them which secondary school they will attend from September.
The Department of Education has admitted that this year the numbers of pupils left without a school place is "higher than usual". Both the department and the Education Authority have said they are working to resolve the issue.
In an open letter to parents, Mr Pitts said that a "large number of families" had been left "extremely disappointed".
It is understood that some of the pupils affected in Bangor have been offered places in Newtownards and Portaferry, with parents left angered by the additional travelling times imposed on their children as a result of the decision.
Mr Pitts told BBC News NI the school has calculated there are "over forty families from Bangor alone who will not gain a place in our school" and children "will be walking past this school to go to a bus stop to travel elsewhere".
The Bangor Academy Principal said that the school was refused two requests for a temporary variation in numbers because there is another controlled school within a "reasonable distance".
A reasonable distance is defined as a journey of one hour or less, and no further than 15 miles from the pupil's home.
'Fell to floor in tears'
Stephen Downey, whose daughter has been turned down, said it was "really ridiculous where you can't send your children to school in your own town".
He told BBC's Nolan Show that it was a case of "déjà vu" after his daughter was forced to go to primary school in Newtownards, despite living in Bangor.
"The whole system is flawed. You have a huge amount of families who are stressed," Mr Downey said.
"Nobody wants to make a decision (in the absence of a minister) - so they are saying no to everything.
"At the moment we are being forced to go to another school that we don't really want to go to."
Another parent, Eileen Reid, said she was "furious" after receiving a letter simply stating that her daughter had not obtained a place at either of her two choices - Bangor Academy or Glenlola Collegiate.
"My daughter just crumbled and fell to the floor in tears and said 'Mummy I have no school'," she said.
Ms Reid said she had been forced to spend Monday travelling between different schools to ask if there is an available space for her daughter from September.
"Nobody is talking to us. We hardly slept over the weekend.
"Nobody had the decency to put a member of staff on on Saturday to speak to us," she added.
Mr Pitts said Bangor Academy had received an unprecedented amount of applications.
"We have made two official requests for a temporary variation in numbers to accommodate the extra places but both requests have been refused," he said.
"We have made everyone aware that this situation is intolerable and, whilst the department is operating within the policy, they are not looking at this from a local and common sense perspective."
Mr Pitts said that without an Executive at Stormont and an education minister in place, there is "nobody willing to make a sensible decision in support of local families from Bangor."
In the letter to parents he said: "It is important for you to note that this is not a school decision and we will do everything in our power to support you."
The principal has urged parents to contact the department's school admissions team, local MLAs and to ultimately consider formally appealing the decision.
In a statement, the Education Authority said it was working with parents and schools to "ensure pupils are allocated places".
"EA has processed applications from over 22000 pupils transferring from P7 to Year 8.
"Around 300 pupils have not been allocated a Year 8 place. Parents have been notified of available school places for consideration."
A spokeswoman for the Department of Education said: "There are always a number of unplaced children at the end of the post primary admissions process, however, this year there are higher than usual numbers.
"DE will continue to work with the EA in analysing the impact of this year's process and approving additional places where they are needed. DE appreciates the uncertainty and disappointment for some pupils and parents and hopes this can be alleviated in the coming weeks."