PCTs were given£300m of money to be spent on public health under the Choosing Health white paper, but it was not ringfenced.
At the annual conference of the Society of Sexual Health Advisers last week, president Jamie Hardie said: 'At a time when the cases of sexually transmitted diseases, especially chlamydia, among young people, are rising in a worrying fashion, it is important to discover where the missing millions have gone.'
Mr Hardie called on the government to ringfence money for sexual health to ensure primary care trusts spend money in that area.
Mr Hardie said the UK's 500-strong workforce of sexual health advisers was being badly affected by cash-strapped acute trusts and PCTs despite the rise in sexually transmitted infections.
The SSHA - a professional section of the union Amicus - has also written a letter to public health minister Caroline Flint calling on her to investigate where the money has gone.
At the conference, delegates were told of cuts to sexual health services across the country, including the proposal by Newham University Hospital trust in East London to disestablish its sexual health advisory team..
The conference also heard from staff at Guy's and St Thomas's foundation trust in London, where posts were being frozen and cut at sexual health clinics.