More than one in ten claimed to not know how to put a condom on while almost a quarter believe wrongly that other forms of contraception could protect them from STIs.
According to the Health Protection Agency, cases of syphilis, genital warts, chlamydia and herpes all increased in 2004-5.
Over a third of students thought latex condoms had holes in them large enough to let the HIV virus slip through. Seven respondents even thought that condoms could be washed and reused.
Both the NUS and THT argue that the survey's findings show a need for sex education to be improved in schools.
Lisa Power, head of policy at THT, said: "University students are no smarter than many other young people when it comes to sexual health. They are just as likely to believe myths about condoms and to have got more of their sex education in the playground than the classroom.
"We spend a fortune educating students, but leave them ignorant about key issues in their adult lives. It's hardly surprising that rates of sexually transmitted infections are soaring."
Veronica King, NUS vice president of welfare at the NUS, added that the poll serves as a "timely reminder" of the need for good sex education.
"Clearly many more resources are needed to improve awareness," she said.
"To ensure that the whole student population is healthy and behaving responsibly there is more to be done in encouraging discussion and continuing education on the sometimes taboo subject of sex and sexual health."
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