Researchers spoke to 8,500 students in 91 secondary schools in Youth 2012, the third in the Youth 2000 Survey Series. The previous two were conducted in 2001 and 2007.
It says 96 per cent of students reported they were not trans, while three per cent were not sure.
The results in regards to same-sex attraction mirrored the 2007 study, with four per cent of students saying they are attracted to the same sex.
Four per cent of students are not sure of their sexual attraction, or attracted to neither sex.
The Adolescent Health Research Group has found young women are more likely to report they are attracted to other women, at 4.5 per cent, compared to 2.5 per cent of male youths surveyed.