Female pupils admitted they were involved in minor but persistent rule-breaking, from shouting out in class and forgetting homework to turning round in their seat, throwing things and interrupting the teacher.
The findings challenge popular views about "good" and "bad" pupils, reigniting the debate about stereotyping pupils on the basis of gender.
There is also concern over the fact that boys are four times more likely to be excluded from secondary school than girls as a result of disruptive behaviour.
The study, by Gillean McCluskey of Edinburgh University, found that more girls than boys were missing from classes without permission and revealed a deep dissatisfaction among pupils with school approaches to discipline.
"The findings call into question many current assumptions," Dr McCluskey states. She presented her work at the international Inclusive and Supportive Education Congress (ISEC) in Glasgow last week (page four), and said that the research strengthened arguments for the re-examination of Scotland's recently introduced guidance on exclusion.
"The distinctions between disrupted and disruptive pupils emerge as much more complex than previously recognised," Dr McCluskey commented.
"Perceptions of young women's involvement in troublesome behaviour and non-attendance come under particular scrutiny."
The research involved 46 pupils aged 13-15 from four Scottish secondary schools, two of which had low levels of exclusion and two with higher levels.
A focus group was set up in each school and pupils were asked for their views on different aspects of disruption, the way it was handled by school managers and the effectiveness of the exclusion process. They were also asked to detail their own involvement in any disruptive behaviour or unauthorised non-attendance. Until now, there has been very little research into the views of non-excluded pupils on discipline.
While pupils reported little direct involvement in behaviour viewed as seriously unacceptable by schools, they confessed to being involved in the types of behaviour that make teachers' lives difficult.
"Young women are much more disruptive than would be predicted from in-school, local authority or national records on disruption and disciplinary exclusion," Dr McCluskey said. "Considered in the light of increasing concern about violence and women, this may call into question widespread and powerful conceptions of disruption as a primarily male phenomenon associated with working class rejection of school."
Contrary to expectations, pupils in the schools known to have lower levels of disruption and higher attainment levels did not express greater satisfaction with overall discipline. In fact, the research revealed a sense of frustration and turbulence in secondary schools. Dr McCluskey observed: "The strength of reaction to the question suggests that a broad range of pupils has concerns about approaches to disruptive behaviour."
Systems for dealing with disruption were often derided and the effectiveness of official exclusion policies was strongly challenged.
Exclusion was viewed as serious and as a punishment, but was seen as largely ineffective. Pupils complained about lack of consistency from teachers in dealing with disruptive pupils and a lack of teacher strictness.
Dr McCluskey said: "It should be of immediate concern to schools that disciplinary exclusion procedures, a central and long-established part of the school discipline process, are seen simultaneously as significant and yet ineffective. There is, therefore, a need for a measured reappraisal of the aims and use of this sanction of last resort."
A spokeswoman for the Scottish Executive said: "We expect all children to behave in school. There is no room for indiscipline." The HMIE report in March had concluded that, on the whole, schools tackled indiscipline effectively, she added.