A total of 58% of GPs responding to the survey said they had experienced 'inappropriate' pressure to cut admissions from the quality and productivity indicators introduced last year.
Just 15% of the 667 GPs surveyed believe the targets have benefited patients.
The indicators, which account for 10% of all QOF points, were unveiled less than a month before the 2011/12 GP contract began, bypassing the usual two-year NICE appraisal process.
The targets aim to avoid inappropriate referrals and emergency admissions, and to lower prescribing costs.
GPs responding to the survey described 'constant pressure to justify referrals and admissions, and pressure to avoid them'. A total of 71% of GPs said funding did not reflect the workload involved.
The poll also revealed wider disaffection with the QOF, as 83% reported overall QOF workload had risen in the past three years. GPs said QOF now requires 'huge and relentless effort' for 'impossible targets'.
Dr Rob Barnett, secretary of Liverpool LMC, said: 'GPs should never let QOF interfere with the way they manage a patient.'
On paper, the indicators promoted 'very good clinical practice', he said. But the 'continually changing' nature of QOF puts 'more demands on practices', he added.
Dr Rachel McMahon of Cleveland LMC said: 'This is a concern. GPs should always put patients first.' She said QOF changes should be 'at maximum every other year'.
GPC deputy chairman Dr Richard Vautrey insisted practices must be allowed to contribute to local plans to meet the targets, and should contact LMCs if they were not.
Other GPs backed the targets. Dr Georgina Brown, vice chairwoman of Glasgow LMC, said feedback from local GPs had been positive.
'We worked with secondary care to agree referral protocols that were practical, workable and appropriate,' she said.
A DH spokeswoman said: 'These indicators are not about putting pressure on practices, but ensuring they are reviewing admissions and referrals that they signed up to as part of the GP contract.'