An insurance company has warned 1,000 GPs not to administer the swine flu vaccine.
The HSE plans to enlist family doctors to give the swine flu vaccine to patients with pre-existing medical conditions.
But an insurance company which covers around 1,000 of the 2,200 to 2,500 GPs in the country advised them not to sign up for the work because of legal indemnity issues.
The HSE has given GPs until today to sign up to give the vaccine to 400,000 of their patients with certain medical conditions from next week.
Medisec Ireland, which covers around 1,000 GPs, told their members yesterday not to sign up until all indemnity issues were resolved.
GP sources said last night this may lead some doctors who have signed up to withdraw their participation in the programme.
In a letter to the doctors Medisec said it was unclear where a GP would legally stand if they exercised their discretion not to give the vaccine to their patients.
There are also unresolved legal issues around the doctors identifying and offering the vaccine to at-risk patients.
The company said the Irish Medical Organisation had been trying to negotiate an acceptable resolution to the serious medico/legal issues with the HSE, but had not been successful.
Other concerns relate to the cost of legal representation for doctors who may find themselves before their disciplinary body the Medical Council if they fail to give the vaccine to a patient.
They could also have to go before the same body for exercising their clinical judgment not to administer the vaccine to a patient of another doctor who had been referred to them.
The letter to GPs said that while the administration of the vaccine would be deemed normal work and covered by a doctor's policy, the outstanding issues of concern might not fall into this category due to the amount of work involved and could lead to "adverse indemnity consequences".
It added: "Accordingly, in the circumstances, we do not recommend our members to sign up for the programme until all issues have been resolved."
The other company indemnifying doctors, the Medical Protection Society, is believed to have indicated GPs could go ahead with the vaccinations.
The HSE may have to extend today's deadline for more clarification. It plans to publicise the rollout of the vaccine to at-risk patients tomorrow.