The HSE has rejected 19 GPs who signed up to provide free visits to under-sixes because they included a letter of protest with their completed contract form.
A spokeswoman for the HSE confirmed it received around 30 signed contracts from GPs which also contained the letters stating they believed providing free visits to healthy under-sixes at the "expense of sicker or more needy patients" was morally wrong.
The letter, which the National Association of General Practitioners (NAGP), urged its members to include when returning their contract, also said they had been coerced into signing the new contract.
"Having raised my concerns regarding patient safety, I will not be accepting responsibility for any negative incidents relating to patient care which arise as a result of this scheme. It is my opinion that since I have clearly stated in advance the risk to patients arising from this decision to proceed with this scheme, the burden of responsibility for patient safety now rests solely with your department and the HSE."
The HSE said yesterday that of the 30 GPs who included the letter, around 11 have already withdrawn these conditions and their contract applications are now being processed.
The spokeswoman told the Irish Independent: "The HSE is pleased the GPs in question have indicated their intent to provide services to children under six and contract applications will be processed as soon as the conditional nature of their contract application and the insertion of extraneous conditions are withdrawn."
It is understood that in response to the accompanying letters the HSE informed the doctors that because of the conditional nature of acceptance it could not accept their signed contract.
The HSE said if they sent the contract again, without the letter, they would be accepted into the scheme which begins in July.
The doctors' applications would be then processed in a timely fashion.
The latest twist comes as the number of GPs who have signed contracts to provide the free visits rose to 80pc nationally yesterday.
It means that 1,946 of 2,430 have agreed to provide the scheme.
However, just nine out of 52 GPs in south Tipperary have signed up.
The HSE said around 58,923 of the eligible 270,000 children have registered.
It is expected there will be a surge in registrations over the weekend in advance of the start of the scheme on July 1.
However, it now looks like many parents will not have registered by the start-up date and will continue to pay a private fee if the child needs to be seen by a GP.