Currently, family doctors receive extra money if they give sufficient numbers of children particular vaccines.
These include the combined vaccine for diphtheria, tentanus and polio and the controversial combined jab for measles, mumps and rubella.
Currently, GPs are paid a standard amount once 70% take-up of the MMR vaccine is achieved and higher payments once take-up tops 90%.
Speaking in a House of Commons Adjournment Debate on Tuesday, Dr Evan Harris, the Liberal Democrat health spokesman, added his voice to calls for the abolition of the current scheme.
He said: "Immunisation target payments are a conspiracy theorist's paradise and they pollute the doctor-patient relationship.
"How can we expect parents to believe they are getting the best independent advice from their GP, when the spectre of financial incentives hangs over the consultation?"
Dr Harris also criticised GPs who suspend patients from their lists in order to achieve immunisation targets.
"It is totally unacceptable and wholly unethical for practices to strike families off their list for refusing to accept immunisation, or to suspend children temporarily from their lists in order to claim the immunisation target payment.
"The GMC and primary care trusts must re-issue urgent guidance and clamp down on any such practices."
Doctors' move
The British Medical Association's GP Committee has written to the Department of Health calling for a "moratorium" on immunisation target payments.
If agreed, family doctors would continue to encourage the take up of MMR and other vaccines but would not be financially penalised if parents - possibly influenced by adverse publicity - decided against immunisation.
Leeds GP Dr Robert Addlestone, said that doctors were being pressured into recommending MMR by the prospect of financial penalties.
Although he thought MMR was safe, he said parents should be able to choose whether their child had the jab.
He said: "I think it's just morally and ethically wrong that the target payments should be tied up with having to persuade parents to have the MMR vaccine.
"Patients should not be affected by our financing. GPs shouldn't be thinking about finance when talking to parents about this."