At least 800 primary school children may not be transferring from primary to secondary school each year, new figures show.
However, the real number may be significantly higher as a comprehensive system to track children's progress in the education system has yet to be put in place.
Figures compiled by school principals in census returns at the end of September 2005 show that at least 260 children who left primary school in 2005 did not go on to any other school.
The destination of a further 543 children was "unknown", according to principals.
The fall-off between the transition from primary to secondary is greatest in areas of highest deprivation, research shows.
The disappearance of students between primary and secondary levels raises a number of issues such as concerns about the protection of vulnerable children and whether the State is fulfilling its duty to provide education to all children.
The figure also broadly tallies with previous estimates by the Economic and Social Research Institute (ESRI) that about 1,000 children a year are failing to make the transition between primary and secondary schools.
The Department of Education, meanwhile, says it would be inaccurate to claim for certain that all children classified under the "destination unknown" category failed to transfer to secondary level.
It says it is working to develop an accurate database that would allow for improved tracking of students after they leave primary school.
In the meantime the department says it has taken a number of measures to improve school completion, such as the establishment five years ago of the National Educational Welfare Board (NEWB), with a remit of monitoring school attendance and tackling absenteeism.
The chief executive of the NEWB, Eddie Ward, said the figures were worrying and a key challenge was ensuring parents were aware of the importance of a proper education for their children.
He said this challenge was also likely to grow with the increasingly diverse school-going population, as there was evidence of differing attitudes towards the importance of education in different parts of the world.
Mr Ward also underlined the importance of having a comprehensive tracking system to ensure children's educational needs are being met, and also to allow authorities to ensure schools could plan for the future.
Groups working with children at risk have been calling on the Government for some time to introduce reforms to combat school dropout rates in poorer parts of the State.
The children's charity Barnardos says interventions to keep children at school need to focus on primary rather than secondary school.
It says most Government-funded "stay-in-school" initiatives are made in secondary school, but this is too late for many children. Research shows that one in three children in primary schools in disadvantaged areas experience severe problems with reading and writing.
It also says Ireland's investment in primary education is well below the averages for most developed countries. Latest figures show the Government invests around €3,042 per student at primary level, compared to €8,131 at third level.