GP's Rate Your PCT survey, the first to let GPs overburdened by monitoring hold a mirror up to NHS managers, found that just 15 per cent had confidence in their PCT or primary care organisation (PCO).
The findings follow criticism of target-driven, inappropriate management at Mid Staffordshire NHS Foundation Trust.
The survey, conducted between October 2009 and January this year, attracted more than 1,650 responses from GPs, practice managers and other practice staff. A total of 73 per cent of GPs who responded, and 77 per cent of partners who completed the survey, had no confidence in their trust.
In total, 85 per cent of GPs rated their trust's overall performance as 'fair' or 'poor', and ratings across a range of key areas, including financial management, leadership and commissioning, were damning.
The survey reveals an alarming picture of clinical disaffection and mistrust. Dedicated individual trust staff are shown as powerless against an inflexible system, with rapid employee turnover, top-down commands and a focus on imported models.
One GP principal said: 'Ours is a forward-thinking, dynamic PCT but too focused on American models of care. Could be excellent if not so distracted.'
Another GP principal said: 'Poor management that would not survive in the private sector.'
The DoH will consult on recommendations from the Francis inquiry into Mid Staffordshire that senior managers should be subject to a professional body with disciplinary powers.
A DoH advisory group on assuring the quality of senior NHS managers also called last week for much tighter controls and possible formal regulation.
Dr Richard Vautrey, GPC deputy chairman, said the poor ratings were no surprise.
'GPs feel very frustrated about the way PCTs seem to make providing services to patients more difficult rather than less,' he said. 'For real change in the relationships we need a change in philosophy at the centre.'
A DoH spokesman said: 'The NHS has had record investment. The challenge for PCTs is to accelerate NHS improvements. Where general practice responds and delivers high-quality services they will be supported by their patients, the local NHS and the government.'
David Stout, director of the NHS Confederation's PCT Network, said: 'We know from last year's assessment of English PCTs under the World Class Commissioning assurance programme and the DoH's practice-based commissioning survey, that PCTs have generally established good working relationships with clinicians.'
Many GPs blamed DoH and SHA interference for distorting local health priorities.
Others pointed to cash constraints limiting PCTs' capacity to support innovation.
One GP said: 'The PCT is completely dysfunctional.'
Another said: 'If my practice administrators were as incompetent I would have been out of business long ago.'