The National Anti-Bullying Research and Resource Centre says one in two principals have dealt with homophobic bullying.
New research carried out by the Resource Centre in Dublin City University, also found that homophobic bullying also happened in some primary schools in Ireland.
However, some school principals thought that children were sometimes too young to understand the actual meaning of the words they use.
The study shows that in 11% of cases, principals said that they had dealt with this issue either weekly or monthly and some also indicated that teachers and/or parents had contacted them to raise a concern.
One in six (16%) indicated that they had dealt with an incident they would describe as homophobic bullying at least once during the school year and in a very small number of cases, principals said that they dealt with an incident where one pupil was physically abused because others thought they were gay or lesbian.
Dr James O'Higgins Norman, Director of the DCU Anti-Bullying Centre, says some principals did not regard the use of homophobic language as bullying.
Dr O'Higgins said: "They didn't naturally or automatically see the name calling as some form of homophobic bullying specifically, so that raised some questions in terms of how they understood homophobic bullying.
"But it is an issue that has appeared in primary schools as our research shows now and I think a lot of it relates back to the way that we educate our children about diversity in society and also I suppose specifically in this situation, sexual diversity."