The sexual health charity's survey of PCT sexual health leads and clinicians in genito-urinary medicine (GUM) clinics found that 59 per cent of PCTs had had all or part of their Choosing Health money diverted away from sexual health.
The Disturbing Symptoms survey, carried out annually, also showed that more than two thirds of PCTs had not done a specific needs assessment for sexual health and HIV in the previous year - a dramatic decline on figures from two years earlier which showed that 51 per cent of PCTs had carried out a needs assessment in 2003.
Terrence Higgins Trust chief executive Nick Partridge told HSJ that the findings made 'disappointing reading'.
'In a year when sexual health was made a national priority and Choosing Health money was available locally, there appears to be a disconnect between national policy and local action.'
Mr Partridge called on the government to ringfence money for sexual health. 'Although it is not popular, it would seem to be the only way to ensure money for sexual health services is not diverted elsewhere.'
Nearly half of PCT respondents called for more cash for sexual health and 26 per cent said they wanted sexual health funding ringfenced.
One respondent admitted that the top-slicing of Choosing Health money by their strategic health authority meant that the PCT would not be able to meet the GUM 48-hour access target, or increase chlamydia screening in primary care settings by the government's 2008 deadline.
The survey also showed responsibility for commissioning sexual health services is shifting to non-specialist public health staff within PCTs, with only 14 per cent of survey respondents saying they were specialist sexual health leads.
Asked how payment by results would affect the ability to provide GUM and HIV services, 24 per cent of GUM clinicians said it would have a negative impact while nearly a third said they did not yet know what the impact would be.
Several clinical respondents said payment by results might help if income from GUM services were re-invested in sexual health - but they worried that this would not happen.