NEW education minister Michelle McIlveen has said extra school places will be created to ensure all P7 children secure a spot.
Two hundred and eighty pupils were left without a second level place for September - out of more than 23,000 young people.
Some parents are angry that their children missed out on grammar schools, however.
Almost all grammars operated non-academic criteria after entrance exams were cancelled.
This caused applications to spiral and it is expected there will be a record number of appeals.
These appeals will only be upheld if a school fails to adhere to its published criteria.
The fallout is causing the first major headache for Ms McIlveen.
She pointed out that 99 per cent of children have a place secured, with 85 per cent given their first choice.
There are 2,700 places still available across the north - some in grammars.
The number of unplaced children is similar to previous years.
Ms McIlveen said she understood the disappointment felt by some children and families.
She said now was the time for parents, schools, and education authorities to act promptly to ensure every child could secure a place as quickly as possible.
"Parents may consider lodging an appeal to an admissions appeal tribunal. I would say to parents that nominating further preferences now does not affect an admissions appeal and if it is successful they can still avail of a place at a preferred school. Therefore I would encourage them to nominate places for their children as soon as possible," she added.
The Department of Education can allocate additional places where there is a need and planning for this year's transfer process started in 2019.
Parental preference cannot be modelled, and the absence of entrance tests made this work even more challenging.
"Where there is demand my department will allocate places and in fact have already done so. By the weekend a total of 828 additional Year 8 places had been allocated to schools across Northern Ireland to cater for oversubscription and this will continue. My department will continue to consider where places need to be allocated, taking into account the needs of individual children," Ms McIlveen added.
Professor Tony Gallagher from Queen's University Belfast said the current chaos had occurred despite a claimed over-supply of places.
"Furthermore, for well over a decade we have had a policy entitled ‘every school a good school’ when clearly the public perception of schools remains unfairly unequal," he said.
"All this underlines the inevitable consequence of academic selection, recently highlighted in the Fair Start report on underachievement as contributing to systemic inequality. A return to 11-plus tests will simply reinforce this systemic inequality. At a practical level, further increases in grammar school places will shift resources away from where they are most needed and would be completely contrary to the spirit of the recommendations of the Fair Start report on underachievement."
