The booklet spelt out how young people can talk about sex in confidence with doctors. However, it did not say that sex for under-16s was illegal. It was eventually published by the British Medical Association.
A DoH spokeswoman dismissed claims that ministers had objected, saying the decision not to publish was the HEA's.
But doctors' leaders questioned the Government's committment to reducing teenage pregnancy rates. Dr Fleur Fisher, head of the BMA ethics committee, said: "Action is needed, not words from ministers."