The National Association of General Practitioners has claimed that the Health Service Executive computer system to allow GPs to extend medical cards is "fundamentally flawed".
It said the system does not allow a GP to reinstate a card once that card has been cancelled.
Cards can be extended before they are cancelled or suspended and cards may be reinstated, but GPs claim there are a wide range of problems with the system.
Since the existence of a 2012 agreement between the HSE and the Irish Medical Organisation, which has provided for GPs to extend cards or reinstate cards, was revealed by RTÉ News this week, many GPs have said their attempts to reinstate cards since for patients have not been successful.
Doctors also claim the system for renewals can only be used on a small percentage of a GPs' lists.
The HSE said it will be writing again to GPs to clarify the situation, as not all are fully aware of all of the computer facilities available to reinstate medical cards.
It said that to date 2,008 GPs have reinstated medical cards and 384 sensitive renewals have been completed using the system.
Some GPs say that during the HSE "probity exercise" introduced after the Budget last year, and suspended by the Government in the summer, cancelled cards could not be reinstated.
Other GPs report being able to reinstate patients where cards have been "suspended", either because the HSE thought the patient was dead, or the patient had not replied to correspondence, which could occur if the letter went to the wrong address.
Doctors also say they are not informed when cards are withdrawn by the HSE and that on occasions the valid date on a patient's medical card does not correlate with the HSE system, which shows that it is "invalid".
Earlier this week, the IMO rejected claims that GPs had the ability, up to now, to reinstate or extend discretionary medical cards, despite an agreement with the HSE in February 2012 to permit renewals and reinstatements.
This year, according to the HSE, more than 850 renewals or reinstatements have been performed by GPs using the system.
The Report of the Expert Panel on Medical Need for Medical Card Eligibility, published this week, also sets out the powers available to GPs since 2012.
It said that in February 2012, the HSE entered into an agreement with the IMO whereby GPs, in certain circumstances, can make amendments to the medical card database by temporarily extending card eligibility for four months, or by restoring eligibility to a patient who has had their eligibility removed, due to not responding to renewal notices from the HSE.
In most cases, where a GP amends the medical card database, third-party verification is then sought from the family or nursing home, or the HSE initiates a review of eligibility.
The report said that in 2012, GPs reinstated eligibility in 800 cases where they were of the opinion that eligibility had been removed in circumstances where the applicant had not responded to renewal notices and eligibility should be restored.
An emergency medical card valid for six months can also be issued within 24 hours of a doctor's report being made available in a number of circumstances, for example a person with a serious medical condition in need of urgent care.
The HSE says no GP has the power to overturn a decision of the State to refuse a medical card, due to a person's income level.
But the Executive said GPs have powers to renew or reinstate cards, in certain circumstances, under the agreed Irish Medical Organisation-HSE circular sent to all GPs in early 2012.
