Peter Peacock cited a study by the Nuffield Foundation and the Institute of Psychiatry, which looked at trends in national data on adolescents over a 25-year period.
"They found that parents perceive young people to have less respect and to be less obedient," Mr Peacock said. "But that study also found that young people today are experiencing more emotional and mental health problems.
"I believe mental health issues among pupils is a more serious issue than any of us may hitherto have recognised. It is an area of work I intend to do more on and will be exploring with health ministers over coming weeks."
Mr Peacock said that, while misbehaviour was a trial to other pupils, parents and teachers, the circumstances of culprits had to be considered.
He noted that:
* More than 40,000 Scottish children live in homes where parents misuse drugs or alcohol.
* Around 9,000 children under the age of 16 run away from home every year.
* An estimated 100,000 children live with the domestic abuse of a parent or carer.
* More than 35,000 children are referred to the children's hearings reporters, the majority on care and welfare grounds.
"It is clear that too many children are not having the time of their lives," Mr Peacock commented. But whatever the challenges facing pupils and the challenges they posed for schools, "there is no single magic answer".
He would continue to provide the resources and back the actions schools were taking to improve behaviour, but it was for a school's management to decide what was best and not for him to be "second-guessing" these judgments.
During questions, Mr Peacock was accused of sending out "mixed messages" on social inclusion by saying he would not be looking over headteachers'
The minister said he was trying to avoid that. Despite the "extraordinarily troubled lives" of many children, the priority had to be to keep them in the classroom, receiving intensive support as necessary. "Once they leave the classroom, they leave society almost," Mr Peacock said.
He accepted that some would have to be excluded from mainstream classes and placed in support units or sent to special bases outside the school, before efforts were made to reintroduce them.