David Alexander, convener of the Church of Scotland's education committee, described some authorities as "dilatory" and called for "appropriate action" to ensure they complied.
Inspectors found that almost all authorities had taken action to update their policies in response to Scottish Executive guidance based on the McCabe report - but that action was not universal.
HMI found variable quality in how well schools worked in partnership with parents and other agencies. And its report, published last week, said the take-up of staff development opportunities was also variable and often exclusively targeted at senior staff.
It stated: "There was a need to ensure that all teachers of personal and social education were adequately prepared for contributing effectively to educating pupils about sensitive health issues."
The report added: "It was normal practice for schools to provide parents with information on the content of education, including health education, in the parents' handbook. This was usually issued when the child started school . . .
"Where schools did not provide parents with adequate information on health education, it was difficult for parents to work effectively in partnership with the school on health matters."
However, Mr Alexander said: "Half of schools inspected reported that they provided annual information for parents. While we would expect all schools to be doing this, it still does not square with the information we receive from parents that they do not get this information from schools."
Inspectors also criticised some authorities for ineffective monitoring of the teaching of personal relationships and sex education. "Teachers at the secondary stages in particular commented on the challenge of matching learning and resources to pupils' different levels of maturity," they reported.
"In some schools, pupils felt their education about responsible personal relationships and sexual health prepared them effectively for life after school. Pupils, most often from S4, did recognise that they had learnt some useful facts about this aspect of education.
"However, they frequently criticised aspects of their education about responsible personal relationships and sexual health such as gaps, repetitions and out of date resources."
HMI's findings come amid growing public debate about how the Executive should take steps to combat worrying figures for teenage pregnancies and what some believe is an epidemic of sexually transmitted diseases.
The Executive aims to publish its sexual health strategy by Christmas but has recently come under fire from the Catholic Church in Scotland over pre-school sex and relationships education and the availability of contraception and advice to teenagers under the age of 16.
Mike McCabe, director of education for South Ayrshire and chair of the working group on sex education, said: "It is pleasing to see that the vast majority of local education authorities have revised their advice to schools. Not everyone will have done that and not everyone will have felt they were required to do that. A number of authorities perhaps didn't feel they had to amend what was in their plans."
Mr McCabe said there was evidence of good development of health-promoting schools and of schools working in a coherent framework with other agencies.
"But schools can't do it all on their own - parents have an important role to play and we are opening up discussions with parents that were not always as open as they might have been in the past."
In a separate report on drug education, HMI found that at national and local level there had been extensive action to tackle drug misuse and provide support for schools. But it noted that schools rarely tracked progress and could not measure the impact of drug education. Many were too reliant on worksheets and videos which sometimes lacked credibility with pupils.
Schools often failed to recognise that different pupils had different needs, such as those living in drug-misusing households.