The findings come from the annual Survey of Smoking, Drinking and Drug Use Among Young People which involves more than 6,000 students in 210 secondary schools.
Commissioned by the Health Service Information Centre and carried out by NatCen Social Research, the figures show that only 56 per cent of 11 to 15-year-olds feel they have received enough information about alcohol, 54 per cent about drugs, and 60 per cent about smoking.
Given that almost all of the 210 schools involved had taught all their pupils about these issues at least once in the previous year, the researchers suggest that the problem might be related to the frequency of lessons and discussions.
Also, it seems many pupils do not even remember having these lessons. Even though most schools said that they taught lessons on smoking, drinking and drugs, only just over half of pupils recalled having these lessons. They were most likely to recall lessons on drugs (59 per cent), than on smoking (55 per cent) or alcohol (53 per cent).
Elsewhere, the survey found that 18 per cent of 11 to 15-year-olds said they had smoked at least once – the lowest level recorded since the survey began in 1982.
This continues the decline since 2003 when 42 per cent of pupils admitted to having tried smoking.
However, 22 per cent had tried e-cigarettes at least once, although this figure included most pupils who admitted to smoking cigarettes regularly.
When it comes to alcohol, 38 per cent had tried it at least once – again the lowest proportion since the survey began.
The prevalence of drug use among 11 to 15-year-olds in England had declined between 2001 and 2010 but since then the decline has slowed. In 2014, 15 per cent of pupils had ever taken drugs, 10 per cent had taken drugs in the last year, and six per cent had taken drugs in the last month.
Overall, the estimates from the survey indicate that in England in 2014 around 90,000 pupils aged between 11 and 15 were regular smokers, around 240,000 had drunk alcohol in the past week, 180,000 had taken drugs in the last month, and 310,000 had taken drugs in the last year.
Elizabeth Fuller, research director at NatCen Social Research, said: "Schools should take note of these findings. A substantial minority of young people do not feel they are getting enough information about smoking, drinking and drugs from their school.
"This is of particular importance because we already know from this survey that young people say that schools are an important source of helpful information on these topics – as important as parents, and more so than other relatives, the media and GPs."