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.
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.
"We received an unprecedented amount of applications this year," said Mr Pitts.
"We have made two official requests for a temporary variation in numbers to accommodate the extra places but both requests have been refused.
"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.