Brook, the sexual health charity which commissioned the survey, said schools needed to do more to teach young people how to use condoms correctly.
Only 37 per cent of sexually-active young people reported using condoms every time they had sex. A third of the 16 to 18-year-olds had sometimes put on condoms too late.
The poll of more than 1,300 teenagers also showed the persistence of sexual health myths.
More than half believed that chlamydia, the most common sexually-transmitted infection in the UK, affects only women.
Almost a third thought infections could be picked up from a toilet seat, but a quarter did not know they could be infected through oral sex.
And 54 per cent did not know that the morning-after pill could be taken up to 72 hours after having sex to prevent conception.
The survey comes as a headteacher has defended his school's decision to allow children under 16 to gain access to contraception without parents'
Since Easter, Somervale secondary school in Somerset has been issuing pupils with cards entitling them to free condoms or the morning-after pill.
This week a parent threatened to take the school to court over the scheme, which has been used in other schools since 1999. But Michael Gorman, the head, said: "We do not regret our stance."
The Brook survey showed that school was the most popular source of information on sex and relationships for young people.
Jan Barlow, chief executive of Brook, said the findings were a powerful argument for making sex and relationships education compulsory.