The government is planning to use patient-reported outcome measures (PROMs) to assess care throughout the NHS.
The measures are likely to be extended to primary care and to play a part in evaluating the success of GP consortia.
But GPC deputy chairman Dr Richard Vautrey said the published figures 'showed how unreliable PROMs are for judging quality care'.
Data were published last week on patient views of outcomes of some elective surgical procedures undertaken in 2009/10.
The report by the NHS Information Centre also showed marked differences in outcomes depending on the type of questionnaire used. Dr Vautrey said: 'Clearly those in significant pain who have an operation that removes that pain are going to be far more grateful, and may overlook issues like cleanliness.
'It demonstrates how complex care is and how simplistic PROMs are not a good way of understanding outcomes.'
But health minister Lord Howe said the measures provide vital insight into patients' views of care effectiveness.
'These experimental data will help the NHS build a fuller picture on quality of care,' he said.
When the scheme began, all licensed providers of hip or knee replacements, groin hernia and varicose vein surgery were asked to invite eligible patients to complete a questionnaire.
Patients undergoing hip replacements reported the best health outcomes, with 87 percent feeling their health had improved after the operation, using the EQ-5D Index score.
But scores varied depending on scoring mechanism. The EQ-VAS score, which asks patients to score their health on the day they complete the questionnaire, recorded a lower improvement after varicose vein surgery of just 37.9 per cent of patients.