Persistent disruptive behaviour was the most common reason pupils were sent home, accounting for half of all suspensions and 39% exclusions.
Nearly half of the suspensions were among pupils getting support for special educational needs - who were three times more likely to be suspended than their classmates.
Children on free school meals were also overrepresented, making up a quarter of the school population but 60% of suspensions.
Paul Whiteman, general secretary at school leaders' union NAHT, said schools alone could not address the causes of poor behaviour.
"Schools have a duty to provide a safe environment for all pupils and only use suspensions and exclusions when other options to ensure this have been exhausted," he said.
"The reasons for disruptive behaviour often lie beyond the school gates and have their roots in wider challenges, including everything from poverty to access to support with special educational needs and mental ill-health."
The vast majority of suspensions - nine in 10 - occurred at secondary schools, with Year 9 having the highest rate.
But primary-age suspensions rose too, up 24% on the previous year.
The vast majority (88%) of pupils who were excluded at primary school were getting support for special educational needs, compared with 46% of excluded secondary school pupils.
Research from charity Chance UK, which supports families of excluded children in London, suggests that 90% of children who are excluded at primary school fail to pass GCSE English and maths.
Sophie Schmal, the charity's director, said Thursday's figures revealed a "very concerning picture" - particularly the rise in primary school suspensions.
"Early intervention has to mean early. We can't wait until these children are teenagers to tackle this."