The State indemnified British drug company GlaxoSmithKline from liability from any side effects associated with the swine flu vaccine Pandemrix, which has been linked with the disabling sleeping disorder narcolepsy.
So far, five cases of narcolepsy have been confirmed among teenagers and young adults who received the swine flu vaccine in Ireland, and at least three more cases of suspected narcolepsy are being investigated.
The indemnity clause, signed as part of an advance-purchase agreement, means that any legal actions that might be taken by people alleging a link between narcolepsy and Pandemrix will have to be lodged against the State.
Waiving liability for side effects is not unusual and other countries also agreed to the indemnity clause.
The HSE, on behalf of the Department of Health, also signed an indemnity clause with Baxter Healthcare, the manufacturer of the other swine flu vaccine available in Ireland.
There have been no reports of suspected acute adverse reactions to the vaccine produced by Baxter Healthcare.
Waiving liability for side effects does not absolve the vaccine companies from compliance with the normal quality-assurance standards in the production of vaccines.
At the time agreement was reached with the drug companies to supply the vaccines to Ireland, the Department of Health said the vaccine would be produced "using methods that have been tried and tested" and that these vaccines "have had a very good safety profile".
Last month, the HSE confirmed to the Sunday Independent that they were removing all stocks of Pandemrix from GPs' surgeries.
All GPs who received consignments of Pandemrix were contacted by letter from Dr Kevin Kelleher, the HSE's assistant national director of Population Health and Health Protection, who told doctors that arrangements would be made to collect all stocks from surgeries.
And last week EU drugs regulators ordered changes to the product label for Pandemrix to highlight the potential risk of narcolepsy in children or adolescents.
The decision was based on the preliminary results of studies from Finland, Sweden and France, suggesting a possible link between the vaccine and the sleeping disorder.
In a statement to the Sunday Independent, the HSE said that Ireland received Pandemrix to protect against pandemic influenza on the same terms as other countries who purchased the vaccine.
"As stated publicly at the time, these terms relieved the vaccine manufacturers from liability," the HSE said.
Contacted by the Sunday Independent, the Irish Medicine's Board (IMB) said that they were now following up on, and evaluating, all reports of suspected cases of narcolepsy in those who have received Pandemrix in Ireland.
"Five cases of narcolepsy following vaccination have been confirmed, but a causal association with the vaccine has not been established. The IMB is actively monitoring this issue. . .
"The IMB recommends anyone who may have any concerns to contact their GP."
The board said they were involved in discussions in relation to Pandemrix at EU level and through the European Medicines Agency.
"It is important to note that further data are awaited from ongoing studies and a causal association with vaccination has not been established. The outcome of the ongoing EU review is expected to be available in July."
More than 31 million doses of Pandemrix have been given to people in 47 countries.
The Reuters news agency reported last week that GlaxoSmithKline, which is Britain's largest drugmaker, said that, as of April 5 this year, it knew of 247 cases of narcolepsy in those vaccinated. "It is important to wait for the results of the ongoing European investigation," GlaxoSmithKline said in a statement.
It's been confirmed 27 people were killed by the swine flu virus in Ireland last year.