In many secondary schools, pupils were taught about the biology of sex, but learned little about relationships, according to an Ofsted report, with teenagers saying that the education they did receive was taught "too late".
In other cases, youngsters were not taught enough about the long-term dangers of alcohol and drugs, inspectors said.
The study analysed personal, social, health and economic (PSHE) education in 92 primary and 73 secondary schools in England based on inspections carried out between September 2006 and July last year.
It shows that in more than a third (34%) of the secondary schools visited, students' knowledge of sex and relationship was "no better than satisfactory", while in a further three schools it was rated "inadequate".
The report says: "Students' knowledge and understanding was often good about the biology of sex but weaker about relationships.
"They said that their sex and relationships education was taught too late and there was not enough of it to be useful.
"Discussion was sometimes limited because of the teacher's embarrassment or lack of knowledge. In these schools, the students did not have the opportunity to explore the nature of relationships in any depth. They had not discussed managing risks, saying 'no', negotiation in relationships, divorce and separation, or living in reconstituted families."
Schools often invited speakers in to give sex education classes, the report found, but in some cases these discussions were also "sometimes constrained by embarrassment".
Inspectors concluded that the majority of schools were teaching PSHE well, although in almost one in four of those visited the quality of teaching was "variable" and teachers' knowledge was not good enough.
The report also raises concerns about drug and alcohol education.
In more than half of the secondaries visited, students didn't know enough about the social risks and physical effects of drinking too much.
Many secondary school students thought that heroin and cocaine were responsible for most deaths each year, when the number of deaths attributed to tobacco and alcohol are much higher.
In some schools pupils "had little knowledge about the long-term social consequences of drug and alcohol misuse and the underlying reasons for drug-taking".
The report adds: "In 15 of the schools visited, students' factual knowledge about drugs, including alcohol and tobacco, was inadequate."
The best schools put on drama and music productions, appointed school councils and took part in residential visits to help pupils develop their PSHE skills.
Ofsted chief inspector Christine Gilbert said: "It is pleasing to see that most of the schools visited were good or outstanding at teaching the subject. However, there were some weaknesses and schools should continue to promote professional development in PSHE education so that teachers strengthen their knowledge and skills in the subject.
"The new study programme to improve economic well-being and capability, introduced as part of PSHE in 2008, is not yet well established. In addition, some schools still struggle to teach their pupils effectively about sensitive but important issues, such as the misuse of drugs and alcohol."
PSHE was made part of the national curriculum more than 10 years ago.
A spokeswoman for the Department for Education said: "This report from Ofsted is a useful assessment of PSHE education in schools. We want all young people to benefit from high quality PSHE teaching and we will take this report's findings into consideration as we continue to look at the curriculum across the board. We will make an announcement on future plans for the curriculum as a whole in due course."
A spokesman for the sexual health charity Brook said it was "vital" that education regarding sex and relationships became compulsory in schools.
National director Simon Blake said: "This reinforces what we already know and what young people have been telling us for years - that the education about sex and relationships they receive is simply not good enough.
"It is vital that sex and relationships education (SRE) becomes compulsory in all schools, and that teachers are specially trained to deliver SRE at all stages of their career.
"This would ensure that children and young people learn about relationships, the risks of alcohol and drugs, and not just the biology of reproduction.
"It is unthinkable that, despite report after report finding the same, that SRE remains patchy and at the whim of individual schools."
Family Planning Association chief executive Julie Bentley said: "Delivering SRE in the classroom is a highly skilled job and professionals need to be supported and trained to teach it.
"It's not surprising that teachers with no background in the subject naturally struggle with issues like embarrassment, which with the right training and support are easily overcome."
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