By Nick Triggle
BBC News health reporter
A part of GP pay is now linked to their performance
Doctors in England say they are being unfairly penalised because of a "flawed" patient survey.
The British Medical Association complained the poll, being used to determine their performance-related pay, was too complicated for patients.
The union also said despite more than 2.1m people being quizzed some practices still had too few patients participating to make it fair.
The government said the survey was a "valuable tool".
GP pay has rocketed through the £100,000 barrier since a new contract started in 2004.
Their income is split into three bits - a lump sum, a performance-related element and bonuses for providing extra services, such as minor surgery.
Performance pay makes up just over a third of their total pay of which the views of patients determines about £2,000 for the average GP.
The BMA cited an example of a large practice of 13,000 patients which saw just 41 quizzed.
Union leaders were also left angry that the number of questions rose five-fold to 49.
Dr Laurence Buckman, chairman of the BMA's GP committee, said: "We want patient feedback and surveys can be a good way of getting this."
But he added: "This survey should be scrapped as it's not fit for purpose. The questions can be misinterpreted, the survey is very long and too complicated.
"In some cases the answers of fewer than a couple of dozen patients will have led to a practice losing thousands of pounds in resources.
"Ironically this will make it harder for these surgeries to then improve their access, which is not going to benefit patients."
Overall, nine in 10 patients said they were happy with their care although the ratings were lower when people were asked about booking appointments.
Norman Lamb, Liberal Democrat health spokesperson, also called for the patient survey to be scrapped.
He said: "Many GPs will be fined today a result of a survey that in many cases only represents a fraction of their patients' views.
"The Government keeps telling us that belts are being tightened in these difficult times yet ministers have spent £10m on a survey that very few people actually responded to."
But the Department of Health said there had been more responses to the patient survey than ever before.
A spokesperson said the process, which had been agreed with the BMA, was designed to improve patients' experience of primary care.
Health minister Mike O'Brien said: "The survey is one of the most valuable tools we have for measuring what patients think of their GP practice.
"I congratulate the vast majority of surgeries who are performing well, but it is clear some surgeries now need to look at these results and identify the areas where patients are still dissatisfied."