The Murdoch Children's Research Institute study explored common emotional and behavioural problems and academic performance among eight and nine-year-old children.

The research found about one in five boys and one in seven girls had at least borderline emotional and behavioural problems.

Of the males with emotional and behavioural difficulties, 20 per cent of the sample were 12 months behind their peers in both reading and numeracy, which was assessed using the National Assessment Program Literacy and Numeracy (NAPLAN) tests.

The boys were also three times more likely to be rated by their teachers as having poor English or mathematical skills, compared to males without these problems, the study showed.

"These males were 12 months behind their peers after only three full years of formal schooling," lead author Dr Lisa Mundy from the Murdoch Children's Research Institute said.

Previous research has shown that children with behaviour problems tend to struggle in school but this is the first study to show that boys with emotional problems are also falling behind in their learning.

For girls with emotional and behavioural difficulties, the results were more modest. However, peer problems were associated with lower numeracy scores for girls.

Overall, both boys and girls with total difficulties, hyperactivity/inattention and peer problems were associated with a greater likelihood of below-average English and maths skills according to the teacher report.

Dr Mundy said it was unlikely that increasing academic pressure was causing emotional and behavioural problems a scenario more common in secondary school.

"A more likely explanation is that mental health and behavioural problems are directly contributing to poor academic performance, possibly through reduced attention to school work or school absence," she said.

"Children with emotional and behavioural problems are at high risk for academic failure. This risk is evident in mid-primary schools.

"The size of this association between mental health and academic problems at an early point in education suggests that emerging mental health problems are an essential aspect of child development to be addressed in the primary school system," Dr Mundy said. "This is particularly important given these years are also a time when students can start to disengage from school."

Senior author Prof George Patton said the mid-primary school years were a time when emotional and behavioural problems commonly emerged and these were often the precursor to health problems continuing in adolescence and adulthood.

He said that it is increasingly clear that students will not reach their academic potential unless schools also promote the social and emotional development of students.

The research was part of a larger project called the Childhood to Adolescence Transition Study (CATS), which is following more than 1,200 children through the middle years of childhood and into adolescence. These children were randomly selected from 43 government, Catholic and independent schools in metropolitan Melbourne.