Thousands of public patients risk being removed from waiting lists for surgery or a specialist appointment next year under a 'two strikes and you are out' rule.
The HSE's national service plan, which comes before Cabinet this week, pledges to step up the validation of public waiting lists.
Although this is needed to remove people who no longer need treatment in order to make it more efficient for others, the methods used are now being criticised by doctors.
Tallaght GP Dr Andrew Jordan, who is chairman of the National Association of General Practitioners, said: "There continues to be a dramatic increase in the number of these validation letters sent to GPs throughout the country.
"We have no issue with the validation of waiting lists in itself. However, the validation process adopted by the HSE to validate waiting lists is negatively impacting upon the most vulnerable in society."
The national centralised validation unit has been set up since September and is managed by the National Treatment Purchase Fund.
A spokesman said the unit allows 14 days for a response to the initial validation letter a patient receives.
There is then a further 14 days allowed to respond to a second reminder letter.
"Accordingly, patients will always be given at least four weeks to respond," he said.
"If the patient does not respond to the second letter, the patient and their GP may be informed that the patient will be removed from the waiting list in compliance with national protocol.
"If the patient or GP considers the hospital care is still required, the patient will be reinstated, maintaining their original place on the list."
To date, the unit has been involved in the validation of waiting lists in St James's University Hospital, University Hospital Limerick, Galway University Hospital, St Vincent's University Hospital and Cork University Hospital.
However, Dr Jordan said Health Minister Simon Harris should reform the validation system. If there is no reply, an attempt should be made to contact the patient by phone to ensure the patient has not changed address, or become homeless, he said. Currently the elderly, homeless, minority communities and people who cannot read are losing out.