NHS North West director of commissioning and performance Joe Rafferty has highlighted concerns that a major genitourinary medicine clinic in the city is operating 'well below' the access target.
Although Manchester primary care trust pays for HIV drug treatment at the Manchester Royal Infirmary clinic, there is no specific budget for HIV patient care.
This means sessions for sexually transmitted infections at the clinic are being used for people with HIV.
In a report to the SHA's board for a meeting that took place earlier this month, Mr Rafferty said data from trust submissions indicated that the clinic, run by Central Manchester and Manchester Children's University Hospitals trust, was seeing only 29 per cent of patients within 48 hours.
Mr Rafferty said: 'The continuing and relentless rise in HIV cases and no PCT commissioning and related budget for HIV patient care (drugs but not care are paid for) at Manchester Royal Infirmary means the trust continues to divert sexually transmitted infection sessions to HIV care.'
The most recent figures from the Health Protection Agency, from 2005, show Manchester has the joint second highest rate of HIV diagnoses in England outside London.
Mr Rafferty said in the report that the situation at Manchester Royal Infirmary 'continues to decline'.
But the primary care trust said the data issues 'have been resolved' and a new building will open at the hospital in the spring. The SHA said it believed this would give the clinic extra capacity.
A PCT statement said: 'Manchester PCT has agreed on an investment plan with the trust to address the increasing numbers of people living with HIV who are treated at the site.
'We are confident that the 48-hour access target will be met as required by March 2008.'
The SHA board was told the overall figure for 48-hour access in the North West was 76 per cent in May, compared with the English average of 72 per cent.