It means that 99.9% of parents who applied on behalf of their children have secured a funded nursery place, with just 16 applicants still waiting.
In April, the BBC reported that almost 800 applicants were waiting to find out if they had been successful.
The new education minister, Peter Weir, said he was "delighted" by the update.
"The department and the Education Authority have worked hard to meet demand for pre-school places, including approving or funding additional places across both voluntary and statutory settings," the minister said.
"Pre-school places remain available across Northern Ireland and the Education Authority will continue to work with those parents who have been unsuccessful in securing a pre-school place."
Letters on the outcome of the second stage of the application process were issued to parents on Friday.
Demand for funded pre-school places has risen in recent years and there are a number of criteria to help schools decide which children to admit.
Legislation requires providers to give preference to children from socially-disadvantaged backgrounds, whose parents are in receipt of Income Support or Jobseeker's Allowance.
Further criteria can include whether a child has had a sibling at the school, or how far away they live from the building.
Almost 23,000 children in Northern Ireland have been offered a pre-school nursery education place from September, funded by the Department of Education.