In future, councils that want to use the questionnaire will no longer be able to ask younger children the most controversial questions.
Parents will also be given a much greater say in the involvement of their children in the survey.
The move comes after a team of statistics experts from the Scottish Government reviewed the Evidence to Success survey following complaints from parents.
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 contract to improve the health of residents by ensuring services are directed at genuine problems.
The 24-page survey asked 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 was the section on drinking and smoking habits, drug use, whether they had carried weapons and sexual practices.
The census also asked whether they had been arrested, if they had "attacked someone with the idea of seriously hurting them", or if they had ever turned up at school "drunk, on drugs or high".
Some families 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".
Perth and Kinross Council originally backed the survey - from a Devon-based charity called the Social Research Unit at Dartington - saying it was voluntary and anonymous, with the vast majority of pupils happy to take part. A Scottish Government spokesman also described it as a good example of a local authority engaging with their communities to ascertain what services were needed.
However, a review by the Government's educational analytical services division has recommended significant changes as the survey is extended to other council areas.
Its report states: "When considering applications of the survey in new authorities ... some questions will be put only to children in secondary school.
"Questions have been raised by parents about the explicit nature of questions in relation to risky sexual behaviour asked of children aged 14 and upwards only.
"In light of parental reservations, these questions have been removed as an option for future authorities until such time that alternative options have been reviewed and agreed."
The report states that the survey is not suitable for use with children with moderate to severe cognitive impairments or special educational needs.
However, while recommending better communication with parents, the report ruled out the possibility of parents having to opt in to the survey, rather than the current situation where they are asked if they want to opt out.
Dee Thomas, a parent from Perth and Kinross who has been campaigning against the explicit nature of the survey, welcomed the report.
She said: "My view is that it is a great step forward, but I am still concerned that there is an assumption that pupils will take part unless they opt out.
"I and other parents who raised concerns about this survey were made to feel marginal in the debate and it seems the Scottish Government has only recently realised they were about to roll out a public relations nightmare across Scotland just before the referendum."