Government figures reveal that 70 of these instances, which took place during the 2015/16 school year, were permanent expulsions.
The figures form part of a trend over recent years, with 2,220 exclusions in 2013/14 and 2,250 in 2014/15 for sexual misconduct, which also includes sexual abuse, bullying, graffiti and harassment.
Rape Crisis spokesperson Katie Russell called the figures “concerning”, saying sexual misconduct appears to be “a significant and ongoing issue in schools”.
But she continued: “It’s also encouraging if it’s being taken seriously and dealt with firmly.
The exclusion figures, which were released by the Department for Education yesterday, follow a parliamentary report last year which found that 29% of 16-18 year old girls had experienced unwanted touching at school.
A further 71% of students this age had regularly heard schoolgirls referred to as “slags” or “sluts”.
Russell said the government’s decision in March to make sex and relationships education compulsory in all schools was an “important first step” in addressing the issue.
Official figures reveal that the equivalent of 35 pupils a day are expelled from state schools in England, with 6,685 occasions of expulsions recorded during the 2015/16 school year - up 1,000 from the year before.
Almost 340,000 exclusions were also issued to students over that period.
Reasons for pupils being excluded include bullying, racist abuse and theft, while 730 school kids were permanently expelled for physically assaulting teachers or school staff.
However, some campaigners have criticised the current system as “burningly unjust”, arguing that half of pupils who are excluded have a mental health problem.
According to analysis from the Institution for Public Policy Research (IPPR), one in every two excluded students experience mental health problems, compared to one in 50 pupils in the wider population.
The think tank said this could be as high as 100% once undiagnosed problems are taken into account.
IPPR associate fellow Kiran Gill said that the discrimination of school exclusions was a “crime”, calling on Theresa May commit dedicated funding and “thought-through” solutions to the issue.
Research from the organisation also found that 99% of pupils permanently excluded from mainstream schools will not achieve five good GCSEs - a benchmark often used as a sign of success at school.
Almost two-thirds of the prison population was excluded from school at some point, researchers added.
A Department for Education spokesperson said that the government wants “every child to have access to a good school place where they can learn without disruption and feel safe at school”.
“The rules are clear that exclusion powers should only be used in particular circumstances and decisions to exclude should be lawful, reasonable and fair.”
They added: “Permanent exclusion should only be used as a last resort, in response to a serious breach, or persistent breaches, of the school’s behaviour policy.”