The voluntary questionnaire, which involved children up to the age of 14, was initiated by Perth and Kinross Council as part of a £225,000 initiative to improve the health of residents.
The 24-page survey asks pupils from P5 to S4 about many aspects of their lives and habits including diet, relationships within their families, how they perform at school and issues of self-esteem.
However, the most controversial aspect is the section that touches on drinking and smoking habits, drug use and whether they have carried weapons.
The census also asks whether they have been arrested, if they have "attacked someone with the idea of seriously hurting them", or if they have ever turned up at school "drunk, on drugs or high".
Children were also questioned about their use of specific drugs such as LSD, cocaine, ecstasy, heroin, valium and cannabis and asked how many times they have been arrested in the past year and how many times they have sold drugs.
Some families have opposed the survey, with one parent writing to John Fyffe, Perth and Kinross Council's head of education, saying her son had found the survey "creepy and weird".
"Our son has dwelt on how it must have felt for one boy in his class, whose mother had died, to answer questions about 'can you talk to your mum?' and 'do your parents argue?'," she said.
"He felt affronted that the school could be asking if he took or supplied cannabis or LSD, and what this survey has done is put all of these concepts of tobacco, alcohol, stealing, weapons and bunking off school in the forefront of very young minds."
However, a spokesman for Perth and Kinross Council stressed the survey – called Evidence2Success – was voluntary and anonymous, with the vast majority of pupils happy to take part.
He also said the project was being carried out with Tayside Police, NHS Tayside and a Devon-based charity called the Social Research Unit at Dartington, which encourages the greater use of evidence when planning public services.
"In order to design support services effectively, reliable evidence about the lives of local children and young people is required," said the spokesman.
"We needed to build up a picture of the views and experiences of young people across our different communities, and the well-being survey is allowing us to do that.
"Children completed the wellbeing survey confidentially and the results will be recorded, analysed and reported anonymously. Participation was not compulsory and parents were informed about the survey and were offered the chance to opt-out their children.
"Children taking part also had the option to exercise their right not to participate, to skip any questions they did not want to answer or to stop completing the well-being survey at any stage."
A Scottish Government spokesman said: "This is a good example of a local authority engaging with their communities to ascertain what services are needed in their communities.
"This work will help give young people a voice in early intervention and prevention services, and whether these are in the right places, and supporting the right people.
"Neither the Scottish Government nor Perth and Kinross Council recognise the claims being made about this piece of work."