The survey of almost 800 Victorian students found 72 per cent of year 9 boys and 65 per cent of year 9 girls had engaged in covert bullying, such as spreading rumours or excluding other children.
Lead researcher, Professor Sheryl Hemphill, said it was surprising to find more boys than girls engaging in this type of bullying.
"Covert bullying was always thought to be predominantly done by girls, but our figures show for the first time that boys are actively engaging in this behaviour," she said.
The study also found children who cyberbully are more likely to go on to use cannabis and engage in crime and violence, while cyberbully victims are more likely to be depressed and cause self harm.
In the past year, more than a quarter of year 9 boys engaged in traditional bullying, with 27 per cent physically or verbally bullying another child. This compared with 14 per cent of year 9 girls.
More girls than boys were bullied in the past year, with 36 per cent of girls compared to 29 per cent of boys subjected to traditional bullying in year 9.
Twenty one per cent of girls and 12 per cent of boys were cyberbully victims in year 9.
Professor Hemphill said the findings would affect how experts thought about ways to prevent bullying across Australia.
The 10-year study began in 2002 and tracks the students from age 10 to 19.
It has been conducted by the Australian Catholic University with Deakin University and Murdoch Children's Research Institute.
The findings will be presented to the National Centre Against bullying conference on June 15-16 - an initiative of the Alannah and Madeline Foundation - and will be used to help protect children from being bullied.